Atomistry » Iron » PDB 7pq1-7qh2 » 7qbs
Atomistry »
  Iron »
    PDB 7pq1-7qh2 »
      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: Wed Apr 5 04:02:21 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy