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Iron in PDB 9gm3: Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla

Enzymatic activity of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla

All present enzymatic activity of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla:
1.8.98.7;

Protein crystallography data

The structure of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla, PDB code: 9gm3 was solved by E.De La Mora, J.Ruel, A.Usclat, L.Martin, P.Amara, B.Morinaka, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.06 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.664, 62.73, 116.549, 90, 117.84, 90
R / Rfree (%) 19.3 / 21.3

Other elements in 9gm3:

The structure of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla (pdb code 9gm3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla, PDB code: 9gm3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 9gm3

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Iron binding site 1 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:21.3
occ:1.00
FE1 A:SF41001 0.0 21.3 1.0
OXT A:SAH1006 2.3 20.5 1.0
N A:SAH1006 2.3 20.4 1.0
S4 A:SF41001 2.4 21.1 1.0
S3 A:SF41001 2.4 21.4 1.0
S2 A:SF41001 2.4 21.6 1.0
FE3 A:SF41001 2.8 21.5 1.0
FE2 A:SF41001 2.9 20.8 1.0
FE4 A:SF41001 2.9 20.4 1.0
C A:SAH1006 3.0 20.0 1.0
CA A:SAH1006 3.1 19.5 1.0
SD A:SAH1006 3.3 19.2 1.0
CG A:SAH1006 3.6 17.9 1.0
CB A:SAH1006 3.9 18.1 1.0
S1 A:SF41001 4.1 21.0 1.0
NH2 A:ARG141 4.1 23.6 1.0
O A:SAH1006 4.2 21.1 1.0
SG A:CYS18 4.5 19.2 1.0
CB A:ASN107 4.7 18.5 1.0
O A:GLY73 4.7 19.9 1.0
C2' A:SAH1006 4.8 19.7 1.0
C3' A:SAH1006 4.9 19.8 1.0
C5' A:SAH1006 4.9 19.6 1.0
NH1 A:ARG141 4.9 22.9 1.0
SG A:CYS22 4.9 20.3 1.0
ND2 A:ASN107 5.0 20.8 1.0
CZ A:ARG141 5.0 24.7 1.0

Iron binding site 2 out of 16 in 9gm3

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Iron binding site 2 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:20.8
occ:1.00
FE2 A:SF41001 0.0 20.8 1.0
SG A:CYS22 2.3 20.3 1.0
S4 A:SF41001 2.3 21.1 1.0
S3 A:SF41001 2.3 21.4 1.0
S1 A:SF41001 2.4 21.0 1.0
FE3 A:SF41001 2.8 21.5 1.0
FE4 A:SF41001 2.8 20.4 1.0
FE1 A:SF41001 2.9 21.3 1.0
CB A:CYS22 3.1 18.3 1.0
NH2 A:ARG141 3.9 23.6 1.0
N A:CYS22 3.9 19.8 1.0
S2 A:SF41001 4.0 21.6 1.0
CA A:CYS22 4.1 20.3 1.0
NH1 A:ARG141 4.1 22.9 1.0
CZ A:ARG141 4.2 24.7 1.0
CB A:LEU20 4.3 19.6 1.0
OXT A:SAH1006 4.4 20.5 1.0
SG A:CYS18 4.7 19.2 1.0
CB A:CYS25 4.7 18.2 1.0
SG A:CYS25 4.8 20.9 1.0
CD1 A:LEU20 4.9 20.9 1.0
N A:SAH1006 4.9 20.4 1.0
C A:LEU20 5.0 20.4 1.0

Iron binding site 3 out of 16 in 9gm3

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Iron binding site 3 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:21.5
occ:1.00
FE3 A:SF41001 0.0 21.5 1.0
S2 A:SF41001 2.3 21.6 1.0
SG A:CYS18 2.3 19.2 1.0
S1 A:SF41001 2.3 21.0 1.0
S4 A:SF41001 2.3 21.1 1.0
FE4 A:SF41001 2.7 20.4 1.0
FE2 A:SF41001 2.8 20.8 1.0
FE1 A:SF41001 2.8 21.3 1.0
CB A:CYS18 3.3 20.4 1.0
N A:SAH1006 3.8 20.4 1.0
S3 A:SF41001 3.9 21.4 1.0
CE2 A:TYR28 4.1 23.8 1.0
O A:LEU20 4.2 21.2 1.0
O A:HOH1120 4.5 20.8 1.0
CB A:LEU20 4.5 19.6 1.0
ND2 A:ASN107 4.6 20.8 1.0
C A:LEU20 4.6 20.4 1.0
CD2 A:TYR28 4.7 22.8 1.0
CA A:CYS18 4.7 20.9 1.0
N A:LEU20 4.8 20.7 1.0
SG A:CYS22 4.8 20.3 1.0
SG A:CYS25 4.8 20.9 1.0
CA A:LEU20 4.8 19.9 1.0
OXT A:SAH1006 4.8 20.5 1.0
C A:GLY73 5.0 20.2 1.0

Iron binding site 4 out of 16 in 9gm3

Go back to Iron Binding Sites List in 9gm3
Iron binding site 4 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:20.4
occ:1.00
FE4 A:SF41001 0.0 20.4 1.0
SG A:CYS25 2.3 20.9 1.0
S2 A:SF41001 2.3 21.6 1.0
S3 A:SF41001 2.3 21.4 1.0
S1 A:SF41001 2.3 21.0 1.0
FE3 A:SF41001 2.7 21.5 1.0
FE2 A:SF41001 2.8 20.8 1.0
FE1 A:SF41001 2.9 21.3 1.0
CB A:CYS25 3.1 18.2 1.0
S4 A:SF41001 4.0 21.1 1.0
CD2 A:TYR28 4.0 22.8 1.0
CE2 A:TYR28 4.1 23.8 1.0
CA A:CYS25 4.3 19.1 1.0
CE A:MET27 4.3 27.3 0.6
CE A:MET27 4.4 27.5 0.4
SD A:SAH1006 4.4 19.2 1.0
CB A:CYS22 4.7 18.3 1.0
N A:SAH1006 4.7 20.4 1.0
SG A:CYS22 4.8 20.3 1.0
C8 A:SAH1006 4.9 18.2 1.0
SG A:CYS18 5.0 19.2 1.0
OXT A:SAH1006 5.0 20.5 1.0

Iron binding site 5 out of 16 in 9gm3

Go back to Iron Binding Sites List in 9gm3
Iron binding site 5 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:25.2
occ:1.00
FE1 A:SF41002 0.0 25.2 1.0
SG A:CYS327 2.3 24.7 1.0
S3 A:SF41002 2.3 26.3 1.0
S4 A:SF41002 2.3 25.1 1.0
S2 A:SF41002 2.3 26.8 1.0
FE4 A:SF41002 2.7 24.2 1.0
FE2 A:SF41002 2.8 23.8 1.0
FE3 A:SF41002 2.8 23.7 1.0
CB A:CYS327 3.0 25.4 1.0
S1 A:SF41002 4.0 24.3 1.0
CG2 A:VAL329 4.1 30.1 1.0
CA A:CYS327 4.5 28.0 1.0
O A:HOH1344 4.6 54.4 1.0
CA A:CYS324 4.6 26.6 1.0
N A:VAL330 4.7 28.4 1.0
SG A:CYS354 4.7 24.6 1.0
SG A:CYS333 4.8 21.1 1.0
CB A:CYS333 4.8 21.8 1.0
SG A:CYS324 4.8 24.6 1.0
CD1 A:PHE358 4.9 28.4 1.0
O A:HOH1354 4.9 48.4 1.0
CA A:VAL330 4.9 28.0 1.0
C A:VAL329 4.9 28.7 1.0
CB A:CYS324 5.0 25.1 1.0
O A:CYS324 5.0 25.4 1.0

Iron binding site 6 out of 16 in 9gm3

Go back to Iron Binding Sites List in 9gm3
Iron binding site 6 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:23.8
occ:1.00
FE2 A:SF41002 0.0 23.8 1.0
SG A:CYS333 2.3 21.1 1.0
S4 A:SF41002 2.3 25.1 1.0
S3 A:SF41002 2.3 26.3 1.0
S1 A:SF41002 2.4 24.3 1.0
FE1 A:SF41002 2.8 25.2 1.0
FE3 A:SF41002 2.8 23.7 1.0
FE4 A:SF41002 2.8 24.2 1.0
CB A:CYS333 3.1 21.8 1.0
S2 A:SF41002 4.0 26.8 1.0
N A:GLY335 4.0 22.2 1.0
CA A:GLY335 4.2 23.1 1.0
CA A:CYS333 4.5 23.4 1.0
CB A:MET357 4.5 21.3 1.0
C A:GLY335 4.6 23.9 1.0
CG2 A:THR351 4.7 18.2 1.0
C A:CYS333 4.7 24.2 1.0
N A:GLY336 4.8 23.5 1.0
CG2 A:VAL329 4.8 30.1 1.0
SG A:CYS324 4.8 24.6 1.0
N A:GLY334 4.8 24.3 1.0
SG A:CYS327 4.9 24.7 1.0
SG A:CYS354 4.9 24.6 1.0
CA A:CYS354 4.9 22.1 1.0

Iron binding site 7 out of 16 in 9gm3

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Iron binding site 7 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:23.7
occ:1.00
FE3 A:SF41002 0.0 23.7 1.0
SG A:CYS324 2.3 24.6 1.0
S1 A:SF41002 2.3 24.3 1.0
S2 A:SF41002 2.3 26.8 1.0
S4 A:SF41002 2.4 25.1 1.0
FE4 A:SF41002 2.7 24.2 1.0
FE1 A:SF41002 2.8 25.2 1.0
FE2 A:SF41002 2.8 23.8 1.0
CB A:CYS324 3.2 25.1 1.0
CA A:CYS324 3.5 26.6 1.0
S3 A:SF41002 3.9 26.3 1.0
CG A:GLN350 4.1 28.3 1.0
N A:CYS324 4.1 27.6 1.0
CA A:GLY335 4.2 23.1 1.0
CB A:GLN350 4.4 22.5 1.0
N A:GLY335 4.5 22.2 1.0
CA A:GLN350 4.6 21.1 1.0
SG A:CYS354 4.7 24.6 1.0
CB A:CYS327 4.7 25.4 1.0
SG A:CYS333 4.8 21.1 1.0
C A:CYS324 4.8 26.8 1.0
SG A:CYS327 4.8 24.7 1.0
C A:THR323 4.9 29.7 1.0
O A:CYS324 5.0 25.4 1.0

Iron binding site 8 out of 16 in 9gm3

Go back to Iron Binding Sites List in 9gm3
Iron binding site 8 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:24.2
occ:1.00
FE4 A:SF41002 0.0 24.2 1.0
SG A:CYS354 2.2 24.6 1.0
S2 A:SF41002 2.3 26.8 1.0
S3 A:SF41002 2.3 26.3 1.0
S1 A:SF41002 2.3 24.3 1.0
FE3 A:SF41002 2.7 23.7 1.0
FE1 A:SF41002 2.7 25.2 1.0
FE2 A:SF41002 2.8 23.8 1.0
CB A:CYS354 3.2 22.0 1.0
CA A:CYS354 3.7 22.1 1.0
S4 A:SF41002 3.9 25.1 1.0
O A:CYS354 4.0 22.7 1.0
C A:CYS354 4.2 22.6 1.0
NE2 A:GLN350 4.2 37.7 1.0
CG A:GLN350 4.4 28.3 1.0
CB A:GLN350 4.5 22.5 1.0
SG A:CYS327 4.7 24.7 1.0
SG A:CYS324 4.8 24.6 1.0
O A:HOH1354 4.8 48.4 1.0
CD A:GLN350 4.8 36.3 1.0
SG A:CYS333 4.9 21.1 1.0
N A:CYS354 5.0 20.8 1.0

Iron binding site 9 out of 16 in 9gm3

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Iron binding site 9 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:30.0
occ:1.00
FE1 C:SF41001 0.0 30.0 1.0
SG C:CYS22 2.2 29.0 1.0
S3 C:SF41001 2.3 29.2 1.0
S4 C:SF41001 2.3 28.9 1.0
S2 C:SF41001 2.3 30.7 1.0
FE4 C:SF41001 2.7 29.1 1.0
FE3 C:SF41001 2.8 28.6 1.0
FE2 C:SF41001 2.9 28.4 1.0
CB C:CYS22 3.1 30.1 1.0
NH2 C:ARG141 3.8 30.7 1.0
S1 C:SF41001 4.0 28.1 1.0
N C:CYS22 4.0 31.4 1.0
CZ C:ARG141 4.1 30.9 1.0
NH1 C:ARG141 4.1 29.6 1.0
CA C:CYS22 4.2 31.7 1.0
OXT C:SAH1005 4.3 24.3 1.0
CB C:LEU20 4.3 32.4 1.0
SG C:CYS18 4.6 29.9 1.0
N C:SAH1005 4.8 24.5 1.0
CB C:CYS25 4.8 27.3 1.0
SG C:CYS25 4.8 29.0 1.0
CD1 C:LEU20 4.9 33.2 1.0
NE C:ARG141 5.0 30.8 1.0

Iron binding site 10 out of 16 in 9gm3

Go back to Iron Binding Sites List in 9gm3
Iron binding site 10 out of 16 in the Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Complex Formed Between the Radical Sam Protein Chlb and the Leader Region of Its Precursor Substrate Chla within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:28.4
occ:1.00
FE2 C:SF41001 0.0 28.4 1.0
N C:SAH1005 2.2 24.5 1.0
OXT C:SAH1005 2.3 24.3 1.0
S3 C:SF41001 2.3 29.2 1.0
S1 C:SF41001 2.4 28.1 1.0
S4 C:SF41001 2.4 28.9 1.0
FE4 C:SF41001 2.8 29.1 1.0
FE3 C:SF41001 2.9 28.6 1.0
FE1 C:SF41001 2.9 30.0 1.0
C C:SAH1005 3.0 24.1 1.0
CA C:SAH1005 3.0 23.5 1.0
SD C:SAH1005 3.3 22.8 1.0
CG C:SAH1005 3.6 22.6 1.0
CB C:SAH1005 3.8 22.3 1.0
S2 C:SF41001 4.0 30.7 1.0
NH2 C:ARG141 4.1 30.7 1.0
O C:SAH1005 4.2 24.9 1.0
SG C:CYS18 4.5 29.9 1.0
C2' C:SAH1005 4.7 20.6 1.0
O C:GLY73 4.7 26.0 1.0
CB C:ASN107 4.8 28.3 1.0
C3' C:SAH1005 4.8 21.2 1.0
C5' C:SAH1005 4.8 22.2 1.0
SG C:CYS22 4.9 29.0 1.0
NH1 C:ARG141 4.9 29.6 1.0
CZ C:ARG141 4.9 30.9 1.0

Reference:

J.Ruel, T.Q.N.Nguyen, Y.Morishita, A.Usclat, L.Martin, P.Amara, S.Kieffer-Jaquinod, M.C.Stefanoiu, E.De La Mora, B.I.Morinaka, Y.Nicolet. Peptide Recognition and Mechanism of the Radical S -Adenosyl-L-Methionine Multiple Cyclophane Synthase Chlb. J.Am.Chem.Soc. V. 147 16850 2025.
ISSN: ESSN 1520-5126
PubMed: 40354606
DOI: 10.1021/JACS.4C16004
Page generated: Fri Aug 8 06:24:27 2025

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