Iron in PDB 4k37: Native Ansmecpe with Bound Adomet

Protein crystallography data

The structure of Native Ansmecpe with Bound Adomet, PDB code: 4k37 was solved by P.J.Goldman, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.46 / 1.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.414, 92.405, 94.099, 90.00, 93.03, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 4k37:

The structure of Native Ansmecpe with Bound Adomet also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Native Ansmecpe with Bound Adomet (pdb code 4k37). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Native Ansmecpe with Bound Adomet, PDB code: 4k37:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 4k37

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Iron binding site 1 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.6
occ:1.00
 FE1 A:SF4501 0.0 11.6 1.0
S4 A:SF4501 2.3 11.7 1.0
S2 A:SF4501 2.3 12.6 1.0
S3 A:SF4501 2.3 12.8 1.0
SG A:CYS276 2.3 12.5 1.0
FE3 A:SF4501 2.7 12.6 1.0
FE2 A:SF4501 2.7 13.3 1.0
FE4 A:SF4501 2.8 11.8 1.0
CB A:CYS276 3.4 12.3 1.0
S1 A:SF4501 3.9 13.0 1.0
NE2 A:GLN264 3.9 23.7 1.0
CD2 A:PHE278 4.0 11.5 1.0
O A:HOH991 4.5 32.0 1.0
CD A:GLN264 4.6 19.0 1.0
CE2 A:PHE278 4.6 15.9 1.0
CA A:CYS276 4.7 12.6 1.0
CZ A:PHE306 4.7 11.4 1.0
SG A:CYS255 4.7 19.1 1.0
SG A:CYS330 4.8 12.8 1.0
SG A:CYS261 4.8 12.9 1.0
OE1 A:GLN264 4.9 22.1 1.0
CE2 A:PHE306 5.0 13.9 1.0

Iron binding site 2 out of 24 in 4k37

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Iron binding site 2 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:13.3
occ:1.00
 FE2 A:SF4501 0.0 13.3 1.0
S1 A:SF4501 2.3 13.0 1.0
S3 A:SF4501 2.3 12.8 1.0
S4 A:SF4501 2.3 11.7 1.0
SG A:CYS255 2.3 19.1 1.0
FE3 A:SF4501 2.7 12.6 1.0
FE4 A:SF4501 2.7 11.8 1.0
FE1 A:SF4501 2.7 11.6 1.0
CB A:CYS255 3.5 19.4 1.0
NE2 A:GLN264 3.8 23.7 1.0
S2 A:SF4501 3.9 12.6 1.0
N A:GLY256 3.9 15.1 1.0
C A:CYS255 3.9 19.1 1.0
O A:HOH933 4.0 26.5 1.0
CA A:CYS255 4.2 16.9 1.0
O A:CYS255 4.4 21.6 1.0
CA A:GLY256 4.4 16.7 1.0
CA A:CYS261 4.5 11.4 1.0
N A:THR262 4.7 14.8 1.0
SG A:CYS261 4.7 12.9 1.0
OG1 A:THR262 4.7 26.0 1.0
SG A:CYS276 4.8 12.5 1.0
CB A:CYS261 4.8 12.2 1.0
SG A:CYS330 4.9 12.8 1.0
CD A:GLN264 4.9 19.0 1.0
O A:HOH672 5.0 20.6 1.0

Iron binding site 3 out of 24 in 4k37

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Iron binding site 3 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.6
occ:1.00
 FE3 A:SF4501 0.0 12.6 1.0
S4 A:SF4501 2.3 11.7 1.0
S2 A:SF4501 2.3 12.6 1.0
S1 A:SF4501 2.3 13.0 1.0
SG A:CYS261 2.3 12.9 1.0
FE1 A:SF4501 2.7 11.6 1.0
FE2 A:SF4501 2.7 13.3 1.0
FE4 A:SF4501 2.7 11.8 1.0
CB A:CYS261 3.2 12.2 1.0
CA A:CYS261 3.6 11.4 1.0
S3 A:SF4501 3.9 12.8 1.0
O A:HOH644 4.0 15.9 1.0
CB A:ARG331 4.0 12.1 1.0
N A:ARG331 4.4 12.5 1.0
N A:CYS261 4.5 13.7 1.0
CD A:ARG331 4.5 13.3 1.0
CE2 A:PHE306 4.5 13.9 1.0
CZ A:PHE306 4.6 11.4 1.0
SG A:CYS255 4.7 19.1 1.0
N A:THR262 4.7 14.8 1.0
SG A:CYS330 4.8 12.8 1.0
C A:CYS261 4.8 14.2 1.0
SG A:CYS276 4.8 12.5 1.0
CA A:ARG331 4.8 12.4 1.0
CG A:ARG331 4.8 15.5 1.0
NH1 A:ARG331 5.0 14.7 1.0

Iron binding site 4 out of 24 in 4k37

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Iron binding site 4 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.8
occ:1.00
 FE4 A:SF4501 0.0 11.8 1.0
S1 A:SF4501 2.3 13.0 1.0
S3 A:SF4501 2.3 12.8 1.0
S2 A:SF4501 2.3 12.6 1.0
SG A:CYS330 2.3 12.8 1.0
FE2 A:SF4501 2.7 13.3 1.0
FE3 A:SF4501 2.7 12.6 1.0
FE1 A:SF4501 2.8 11.6 1.0
CB A:CYS330 3.6 12.4 1.0
N A:ARG331 3.9 12.5 1.0
S4 A:SF4501 3.9 11.7 1.0
CA A:CYS330 4.1 13.4 1.0
O A:HOH860 4.1 32.3 1.0
N A:ARG332 4.2 11.0 1.0
C A:CYS330 4.3 14.6 1.0
CA A:GLY256 4.3 16.7 1.0
CE2 A:PHE278 4.4 15.9 1.0
CD2 A:PHE278 4.5 11.5 1.0
CB A:ARG332 4.6 14.0 1.0
N A:GLY256 4.8 15.1 1.0
CA A:ARG331 4.8 12.4 1.0
SG A:CYS261 4.8 12.9 1.0
CB A:ARG331 4.8 12.1 1.0
SG A:CYS276 4.9 12.5 1.0
O A:HOH644 4.9 15.9 1.0
SG A:CYS255 4.9 19.1 1.0

Iron binding site 5 out of 24 in 4k37

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Iron binding site 5 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:16.6
occ:1.00
 FE1 A:SF4502 0.0 16.6 1.0
S2 A:SF4502 2.3 15.8 1.0
S4 A:SF4502 2.3 16.6 1.0
S3 A:SF4502 2.3 16.3 1.0
SG A:CYS348 2.3 18.2 1.0
FE4 A:SF4502 2.7 17.5 1.0
FE2 A:SF4502 2.7 16.9 1.0
FE3 A:SF4502 2.7 15.8 1.0
CB A:CYS348 3.3 15.3 1.0
CA A:CYS348 3.7 14.0 1.0
S1 A:SF4502 3.8 15.5 1.0
O A:CYS348 3.9 14.2 1.0
CE A:LYS352 4.0 28.0 1.0
C A:CYS348 4.1 15.8 1.0
CD1 A:LEU344 4.3 21.0 1.0
CG A:LYS352 4.6 23.8 1.0
SG A:CYS320 4.7 18.9 1.0
SG A:CYS317 4.7 19.4 1.0
CD A:LYS352 4.8 26.1 1.0
SG A:CYS326 4.9 17.3 1.0
NZ A:LYS352 5.0 32.0 1.0

Iron binding site 6 out of 24 in 4k37

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Iron binding site 6 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:16.9
occ:1.00
 FE2 A:SF4502 0.0 16.9 1.0
S1 A:SF4502 2.3 15.5 1.0
S3 A:SF4502 2.3 16.3 1.0
S4 A:SF4502 2.3 16.6 1.0
SG A:CYS317 2.3 19.4 1.0
FE1 A:SF4502 2.7 16.6 1.0
FE4 A:SF4502 2.7 17.5 1.0
FE3 A:SF4502 2.7 15.8 1.0
CB A:CYS317 3.2 19.2 1.0
CA A:CYS317 3.5 22.4 1.0
S2 A:SF4502 3.8 15.8 1.0
CD1 A:LEU344 4.0 21.0 1.0
N A:CYS317 4.1 24.3 1.0
CA A:GLY328 4.3 15.1 1.0
O A:HOH671 4.4 18.7 1.0
N A:GLY328 4.6 15.1 1.0
SG A:CYS348 4.6 18.2 1.0
CB A:CYS320 4.7 23.4 1.0
SG A:CYS326 4.7 17.3 1.0
SG A:CYS320 4.8 18.9 1.0
C A:GLU316 4.8 28.7 1.0
C A:CYS317 4.8 22.3 1.0

Iron binding site 7 out of 24 in 4k37

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Iron binding site 7 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:15.8
occ:1.00
 FE3 A:SF4502 0.0 15.8 1.0
S2 A:SF4502 2.3 15.8 1.0
S1 A:SF4502 2.3 15.5 1.0
S4 A:SF4502 2.3 16.6 1.0
SG A:CYS326 2.3 17.3 1.0
FE4 A:SF4502 2.7 17.5 1.0
FE2 A:SF4502 2.7 16.9 1.0
FE1 A:SF4502 2.7 16.6 1.0
CB A:CYS326 3.2 17.6 1.0
S3 A:SF4502 3.9 16.3 1.0
N A:GLY328 4.1 15.1 1.0
CA A:GLY328 4.3 15.1 1.0
CD2 A:TYR351 4.6 13.7 1.0
CA A:CYS326 4.6 15.0 1.0
SG A:CYS317 4.8 19.4 1.0
C A:CYS326 4.8 19.5 1.0
CB A:TYR351 4.8 12.4 1.0
C A:GLY328 4.9 15.2 1.0
N A:LYS327 4.9 18.8 1.0
SG A:CYS320 4.9 18.9 1.0
SG A:CYS348 5.0 18.2 1.0

Iron binding site 8 out of 24 in 4k37

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Iron binding site 8 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:17.5
occ:1.00
 FE4 A:SF4502 0.0 17.5 1.0
S3 A:SF4502 2.2 16.3 1.0
S1 A:SF4502 2.3 15.5 1.0
S2 A:SF4502 2.3 15.8 1.0
SG A:CYS320 2.3 18.9 1.0
FE1 A:SF4502 2.7 16.6 1.0
FE2 A:SF4502 2.7 16.9 1.0
FE3 A:SF4502 2.7 15.8 1.0
CB A:CYS320 3.1 23.4 1.0
S4 A:SF4502 3.9 16.6 1.0
CE A:LYS352 4.1 28.0 1.0
NZ A:LYS352 4.4 32.0 1.0
CB A:TRP322 4.5 16.4 1.0
CA A:CYS320 4.6 24.2 1.0
CA A:CYS317 4.6 22.4 1.0
CG A:LYS352 4.7 23.8 1.0
N A:PHE323 4.7 21.8 1.0
C A:TRP322 4.8 17.1 1.0
SG A:CYS348 4.8 18.2 1.0
SG A:CYS317 4.8 19.4 1.0
SG A:CYS326 4.8 17.3 1.0
O A:HOH990 4.9 30.4 1.0
CB A:CYS326 4.9 17.6 1.0
CA A:PHE323 4.9 21.0 1.0
CB A:CYS317 4.9 19.2 1.0

Iron binding site 9 out of 24 in 4k37

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Iron binding site 9 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:9.0
occ:1.00
 FE1 A:SF4503 0.0 9.0 1.0
SG A:CYS15 2.2 9.2 1.0
S2 A:SF4503 2.3 10.0 1.0
S3 A:SF4503 2.3 9.1 1.0
S4 A:SF4503 2.3 8.5 1.0
FE4 A:SF4503 2.7 9.1 1.0
FE2 A:SF4503 2.7 9.2 1.0
FE3 A:SF4503 2.7 9.2 1.0
CB A:CYS15 3.3 9.7 1.0
S1 A:SF4503 3.8 9.7 1.0
N A:SAM504 3.9 8.8 1.0
O A:LEU17 4.2 9.9 1.0
CB A:LEU17 4.2 9.4 1.0
CB A:HIS25 4.4 16.4 1.0
C A:LEU17 4.6 10.5 1.0
N A:LEU17 4.7 9.0 1.0
CA A:CYS15 4.7 11.7 1.0
ND2 A:ASN100 4.7 8.3 1.0
CA A:LEU17 4.7 6.1 1.0
SG A:CYS22 4.8 12.7 1.0
O A:SAM504 4.8 9.3 1.0
SG A:CYS19 4.8 9.4 1.0
C A:GLY66 4.9 8.0 1.0

Iron binding site 10 out of 24 in 4k37

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Iron binding site 10 out of 24 in the Native Ansmecpe with Bound Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Native Ansmecpe with Bound Adomet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:9.2
occ:1.00
 FE2 A:SF4503 0.0 9.2 1.0
O A:SAM504 2.3 9.3 1.0
S4 A:SF4503 2.3 8.5 1.0
S3 A:SF4503 2.3 9.1 1.0
S1 A:SF4503 2.3 9.7 1.0
N A:SAM504 2.4 8.8 1.0
FE1 A:SF4503 2.7 9.0 1.0
FE4 A:SF4503 2.8 9.1 1.0
FE3 A:SF4503 2.8 9.2 1.0
C A:SAM504 3.0 7.7 1.0
CA A:SAM504 3.2 8.0 1.0
SD A:SAM504 3.4 11.5 1.0
CG A:SAM504 3.8 9.5 1.0
S2 A:SF4503 4.0 10.0 1.0
CB A:SAM504 4.0 8.2 1.0
NH2 A:ARG134 4.1 10.3 1.0
CE A:SAM504 4.2 9.9 1.0
OXT A:SAM504 4.2 9.9 1.0
SG A:CYS15 4.5 9.2 1.0
O A:GLY66 4.6 9.2 1.0
C2' A:SAM504 4.7 7.9 1.0
CB A:ASN100 4.8 6.1 1.0
C3' A:SAM504 4.8 11.3 1.0
NH1 A:ARG134 4.9 9.1 1.0
SG A:CYS22 4.9 12.7 1.0
CZ A:ARG134 5.0 10.3 1.0
C5' A:SAM504 5.0 11.3 1.0

Reference:

P.J.Goldman, T.L.Grove, L.A.Sites, M.I.Mclaughlin, S.J.Booker, C.L.Drennan. X-Ray Structure of An Adomet Radical Activase Reveals An Anaerobic Solution For Formylglycine Posttranslational Modification. Proc.Natl.Acad.Sci.Usa V. 110 8519 2013.
ISSN: ISSN 0027-8424
PubMed: 23650368
DOI: 10.1073/PNAS.1302417110
Page generated: Sun Dec 13 15:39:03 2020

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