Atomistry » Iron » PDB 7pr2-7qhf » 7qbs
Atomistry »
  Iron »
    PDB 7pr2-7qhf »
      7qbs »

Iron in PDB 7qbs: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.

Protein crystallography data

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs was solved by N.Bernardo-Garcia, C.D.Fyfe, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.33
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 119.29, 119.29, 68.56, 90, 90, 120
R / Rfree (%) 18.2 / 23.5

Other elements in 7qbs:

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. (pdb code 7qbs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 7qbs

Go back to Iron Binding Sites List in 7qbs
Iron binding site 1 out of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:57.2
occ:1.00
 FE1 A:SF4501 0.0 57.2 1.0
SG A:CYS22 2.3 55.2 1.0
S4 A:SF4501 2.3 57.9 1.0
S3 A:SF4501 2.3 57.3 1.0
S2 A:SF4501 2.3 57.8 1.0
FE2 A:SF4501 2.7 57.8 1.0
FE3 A:SF4501 2.8 59.7 1.0
FE4 A:SF4501 2.8 57.4 1.0
CB A:CYS22 3.0 54.1 1.0
S1 A:SF4501 3.9 58.1 1.0
CA A:CYS22 4.1 54.2 1.0
CE A:SAM503 4.3 74.8 1.0
CB A:PRO11 4.6 54.0 1.0
SG A:CYS15 4.8 50.5 1.0
SD A:SAM503 4.8 74.4 1.0
CD1 A:PHE18 4.8 51.6 1.0
SG A:CYS19 4.9 52.9 1.0
CD2 A:PHE24 4.9 63.6 1.0
N A:CYS19 4.9 52.1 1.0
N A:GLY12 4.9 54.1 1.0
C A:CYS22 5.0 55.2 1.0
OXT A:SAM503 5.0 73.7 1.0

Iron binding site 2 out of 5 in 7qbs

Go back to Iron Binding Sites List in 7qbs
Iron binding site 2 out of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:57.8
occ:1.00
 FE2 A:SF4501 0.0 57.8 1.0
S3 A:SF4501 2.3 57.3 1.0
S4 A:SF4501 2.3 57.9 1.0
S1 A:SF4501 2.3 58.1 1.0
SG A:CYS19 2.4 52.9 1.0
FE1 A:SF4501 2.7 57.2 1.0
FE3 A:SF4501 2.8 59.7 1.0
FE4 A:SF4501 2.8 57.4 1.0
CB A:CYS19 3.3 52.0 1.0
O A:HOH651 3.6 63.1 1.0
N A:CYS19 3.8 52.1 1.0
S2 A:SF4501 3.9 57.8 1.0
NZ A:LYS119 4.1 55.7 1.0
CA A:CYS19 4.2 52.0 1.0
OXT A:SAM503 4.2 73.7 1.0
CE A:LYS119 4.2 56.8 1.0
CB A:CYS22 4.3 54.1 1.0
SG A:CYS22 4.6 55.2 1.0
CB A:CYS15 4.7 54.5 1.0
SG A:CYS15 4.8 50.5 1.0
C A:PHE18 4.8 52.4 1.0

Iron binding site 3 out of 5 in 7qbs

Go back to Iron Binding Sites List in 7qbs
Iron binding site 3 out of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:59.7
occ:1.00
 FE3 A:SF4501 0.0 59.7 1.0
S1 A:SF4501 2.3 58.1 1.0
S4 A:SF4501 2.3 57.9 1.0
S2 A:SF4501 2.3 57.8 1.0
OXT A:SAM503 2.3 73.7 1.0
N A:SAM503 2.7 72.8 1.0
FE4 A:SF4501 2.7 57.4 1.0
FE2 A:SF4501 2.8 57.8 1.0
FE1 A:SF4501 2.8 57.2 1.0
C A:SAM503 3.2 73.4 1.0
SD A:SAM503 3.3 74.4 1.0
CA A:SAM503 3.4 73.3 1.0
CG A:SAM503 3.7 74.4 1.0
CE A:SAM503 3.9 74.8 1.0
S3 A:SF4501 3.9 57.3 1.0
O A:HOH651 4.0 63.1 1.0
CB A:SAM503 4.1 73.8 1.0
O A:SAM503 4.4 73.2 1.0
SG A:CYS15 4.7 50.5 1.0
OD1 A:ASP90 4.7 72.0 1.0
C2' A:SAM503 4.8 69.2 1.0
SG A:CYS19 4.8 52.9 1.0
SG A:CYS22 4.9 55.2 1.0
CB A:SER117 5.0 56.6 1.0

Iron binding site 4 out of 5 in 7qbs

Go back to Iron Binding Sites List in 7qbs
Iron binding site 4 out of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:57.4
occ:1.00
 FE4 A:SF4501 0.0 57.4 1.0
SG A:CYS15 2.2 50.5 1.0
S1 A:SF4501 2.3 58.1 1.0
S2 A:SF4501 2.3 57.8 1.0
S3 A:SF4501 2.3 57.3 1.0
FE3 A:SF4501 2.7 59.7 1.0
FE2 A:SF4501 2.8 57.8 1.0
FE1 A:SF4501 2.8 57.2 1.0
CB A:CYS15 3.0 54.5 1.0
N A:SAM503 3.9 72.8 1.0
N A:GLY12 3.9 54.1 1.0
S4 A:SF4501 3.9 57.9 1.0
CA A:CYS15 4.4 55.8 1.0
CA A:PRO11 4.5 53.5 1.0
CB A:ASP90 4.7 65.3 1.0
N A:ASP90 4.7 64.7 1.0
CA A:GLY12 4.7 54.5 1.0
C A:PRO11 4.8 53.9 1.0
CB A:PRO11 4.8 54.0 1.0
OXT A:SAM503 4.8 73.7 1.0
NZ A:LYS119 4.8 55.7 1.0
SG A:CYS22 4.8 55.2 1.0
CE A:LYS119 4.9 56.8 1.0
SG A:CYS19 4.9 52.9 1.0

Iron binding site 5 out of 5 in 7qbs

Go back to Iron Binding Sites List in 7qbs
Iron binding site 5 out of 5 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:64.3
occ:1.00
 SG A:CYS38 2.3 62.7 1.0
SG A:CYS48 2.4 67.0 1.0
SG A:CYS35 2.4 57.2 1.0
SG A:CYS45 2.5 66.3 1.0
CB A:CYS48 3.4 64.9 1.0
CB A:CYS45 3.4 65.0 1.0
N A:CYS35 3.5 57.4 1.0
CB A:CYS38 3.5 62.2 1.0
N A:CYS38 3.5 61.2 1.0
CB A:CYS35 3.6 56.9 1.0
N A:CYS45 3.6 65.0 1.0
CA A:CYS38 3.7 62.6 1.0
N A:CYS48 3.9 63.8 1.0
CA A:CYS35 4.0 56.8 1.0
CA A:CYS45 4.0 65.2 1.0
C A:GLY34 4.2 59.0 1.0
C A:GLY44 4.2 65.5 1.0
CA A:CYS48 4.3 64.9 1.0
C A:TYR37 4.3 60.9 1.0
O A:CYS35 4.4 55.7 1.0
C A:CYS35 4.4 56.2 1.0
CA A:GLY34 4.4 61.3 1.0
CA A:GLY44 4.5 66.0 1.0
C A:CYS45 4.5 66.2 1.0
O A:CYS45 4.7 66.5 1.0
CB A:TYR47 4.7 62.3 1.0
N A:GLY44 4.7 66.5 1.0
N A:TYR37 4.8 58.7 1.0
N A:GLY34 4.8 63.2 1.0
CA A:TYR37 4.9 59.5 1.0
C A:TYR47 4.9 63.7 1.0
CB A:TYR37 4.9 59.0 1.0
N A:TYR47 4.9 65.0 1.0
O A:GLY44 4.9 65.4 1.0
O A:TYR37 5.0 61.5 1.0

Reference:

C.D.Fyfe, N.Bernardo-Garcia, L.Fradale, S.Grimaldi, A.Guillot, C.Brewee, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau. Crystallographic Snapshots of A B 12 -Dependent Radical Sam Methyltransferase. Nature V. 602 336 2022.
ISSN: ESSN 1476-4687
PubMed: 35110733
DOI: 10.1038/S41586-021-04355-9
Page generated: Thu Aug 8 18:10:31 2024

Last articles

Cl in 2Y2H
Cl in 2Y2J
Cl in 2Y2I
Cl in 2Y1X
Cl in 2Y1G
Cl in 2Y1F
Cl in 2Y05
Cl in 2Y1K
Cl in 2XZR
Cl in 2Y08
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy