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Iron in PDB 7qbu: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.

Protein crystallography data

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbu was solved by 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) 44.84 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.779, 79.493, 151.659, 90, 90, 90
R / Rfree (%) 19.1 / 22.5

Other elements in 7qbu:

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Cobalt (Co) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. (pdb code 7qbu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 7qbu

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Iron binding site 1 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.8
occ:1.00
 FE1 A:SF4501 0.0 41.8 1.0
S4 A:SF4501 2.3 42.5 1.0
S3 A:SF4501 2.3 42.0 1.0
S2 A:SF4501 2.3 42.2 1.0
SG A:CYS22 2.4 39.8 1.0
FE2 A:SF4501 2.7 42.8 1.0
FE4 A:SF4501 2.8 41.8 1.0
FE3 A:SF4501 2.8 42.9 1.0
CB A:CYS22 3.2 38.2 1.0
S1 A:SF4501 3.9 42.7 1.0
CB A:PRO11 4.0 41.1 1.0
CA A:CYS22 4.1 39.2 1.0
OH A:TYR115 4.3 44.6 1.0
CE1 A:TYR23 4.5 53.2 1.0
N A:GLY12 4.6 42.1 1.0
CD1 A:PHE18 4.6 40.8 1.0
CD1 A:TYR23 4.7 51.3 1.0
CA A:PRO11 4.7 41.4 1.0
N A:CYS19 4.8 40.2 1.0
SG A:CYS15 4.8 37.0 1.0
SG A:CYS19 4.8 43.0 1.0
CB A:CYS19 4.9 40.9 1.0
CG A:PRO11 4.9 41.0 1.0
C A:CYS22 5.0 40.4 1.0
C A:PRO11 5.0 42.4 1.0

Iron binding site 2 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 2 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.8
occ:1.00
 FE2 A:SF4501 0.0 42.8 1.0
S4 A:SF4501 2.3 42.5 1.0
S3 A:SF4501 2.3 42.0 1.0
SG A:CYS19 2.3 43.0 1.0
S1 A:SF4501 2.3 42.7 1.0
FE3 A:SF4501 2.7 42.9 1.0
FE1 A:SF4501 2.7 41.8 1.0
FE4 A:SF4501 2.8 41.8 1.0
CB A:CYS19 3.2 40.9 1.0
O A:HOH640 3.6 47.9 1.0
N A:CYS19 3.8 40.2 1.0
S2 A:SF4501 3.9 42.2 1.0
CA A:CYS19 4.1 40.7 1.0
NZ A:LYS119 4.1 47.4 1.0
OH A:TYR115 4.2 44.6 1.0
CE A:LYS119 4.3 45.8 1.0
CB A:CYS22 4.5 38.2 1.0
SG A:CYS22 4.7 39.8 1.0
SG A:CYS15 4.9 37.0 1.0
CB A:CYS15 4.9 39.6 1.0
C A:PHE18 4.9 41.1 1.0

Iron binding site 3 out of 10 in 7qbu

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Iron binding site 3 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.9
occ:1.00
 FE3 A:SF4501 0.0 42.9 1.0
OH A:TYR115 1.7 44.6 1.0
S1 A:SF4501 2.3 42.7 1.0
S4 A:SF4501 2.3 42.5 1.0
S2 A:SF4501 2.3 42.2 1.0
FE4 A:SF4501 2.7 41.8 1.0
FE2 A:SF4501 2.7 42.8 1.0
FE1 A:SF4501 2.8 41.8 1.0
CZ A:TYR115 2.8 43.3 1.0
CE2 A:TYR115 3.2 42.5 1.0
O A:HOH640 3.6 47.9 1.0
S3 A:SF4501 3.9 42.0 1.0
O2' A:MTA503 4.0 51.4 1.0
CE1 A:TYR115 4.0 42.4 1.0
C2' A:MTA503 4.3 51.2 1.0
OG A:SER117 4.4 44.4 1.0
CD2 A:TYR115 4.6 41.9 1.0
SG A:CYS15 4.8 37.0 1.0
SG A:CYS19 4.8 43.0 1.0

Iron binding site 4 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 4 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.8
occ:1.00
 FE4 A:SF4501 0.0 41.8 1.0
S2 A:SF4501 2.3 42.2 1.0
S1 A:SF4501 2.3 42.7 1.0
SG A:CYS15 2.3 37.0 1.0
S3 A:SF4501 2.3 42.0 1.0
FE3 A:SF4501 2.7 42.9 1.0
FE1 A:SF4501 2.8 41.8 1.0
FE2 A:SF4501 2.8 42.8 1.0
CB A:CYS15 3.1 39.6 1.0
N A:GLY12 3.8 42.1 1.0
S4 A:SF4501 3.9 42.5 1.0
OH A:TYR115 4.2 44.6 1.0
N A:ASP90 4.3 40.0 1.0
CA A:PRO11 4.3 41.4 1.0
CE2 A:TYR115 4.5 42.5 1.0
CB A:PRO11 4.6 41.1 1.0
CA A:CYS15 4.6 41.0 1.0
C A:PRO11 4.6 42.4 1.0
CA A:GLY12 4.7 43.1 1.0
CB A:ASP90 4.8 39.5 1.0
CE A:LYS119 4.8 45.8 1.0
CA A:GLY89 4.8 42.8 1.0
SG A:CYS19 4.8 43.0 1.0
CZ A:TYR115 4.9 43.3 1.0
SG A:CYS22 4.9 39.8 1.0
NZ A:LYS119 4.9 47.4 1.0

Iron binding site 5 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 5 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine 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, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:46.8
occ:1.00
 SG A:CYS38 2.3 50.9 1.0
SG A:CYS45 2.3 56.8 1.0
SG A:CYS48 2.4 54.4 1.0
SG A:CYS35 2.4 50.2 1.0
CB A:CYS45 3.4 53.6 1.0
CB A:CYS48 3.4 54.5 1.0
CB A:CYS35 3.5 49.5 1.0
N A:CYS38 3.5 49.3 1.0
N A:CYS35 3.5 49.8 1.0
CB A:CYS38 3.6 49.8 1.0
N A:CYS45 3.6 54.0 1.0
CA A:CYS38 3.7 50.0 1.0
N A:CYS48 3.9 53.6 1.0
CA A:CYS45 4.0 53.6 1.0
CA A:CYS35 4.0 50.2 1.0
C A:GLY44 4.1 55.1 1.0
C A:GLY34 4.2 50.2 1.0
C A:TYR37 4.3 48.9 1.0
CA A:CYS48 4.3 55.2 1.0
C A:CYS35 4.4 51.0 1.0
CA A:GLY34 4.5 50.9 1.0
O A:CYS35 4.5 51.6 1.0
CA A:GLY44 4.5 55.5 1.0
C A:CYS45 4.5 53.9 1.0
O A:CYS45 4.6 54.0 1.0
N A:GLY44 4.7 56.0 1.0
N A:TYR37 4.7 48.0 1.0
CB A:TYR37 4.7 46.7 1.0
N A:GLY34 4.7 51.2 1.0
CA A:TYR37 4.8 47.7 1.0
O A:GLY44 4.8 55.6 1.0
CB A:TYR47 4.9 50.0 1.0
C A:TYR47 4.9 52.5 1.0
O A:GLY34 4.9 49.9 1.0
O A:TYR37 5.0 49.2 1.0

Iron binding site 6 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 6 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:47.9
occ:1.00
 FE1 B:SF4501 0.0 47.9 1.0
SG B:CYS22 2.3 40.5 1.0
S3 B:SF4501 2.3 48.5 1.0
S2 B:SF4501 2.3 48.8 1.0
S4 B:SF4501 2.3 48.5 1.0
FE4 B:SF4501 2.8 48.2 1.0
FE2 B:SF4501 2.8 48.7 1.0
FE3 B:SF4501 2.8 48.4 1.0
CB B:CYS22 3.2 39.8 1.0
CB B:PRO11 3.9 52.7 1.0
S1 B:SF4501 3.9 48.4 1.0
CA B:CYS22 4.1 40.2 1.0
OH B:TYR115 4.3 42.1 1.0
CE1 B:TYR23 4.5 51.3 1.0
N B:GLY12 4.5 51.6 1.0
CA B:PRO11 4.6 52.5 1.0
CD1 B:TYR23 4.6 49.8 1.0
CD1 B:PHE18 4.6 42.1 1.0
N B:CYS19 4.8 41.3 1.0
SG B:CYS15 4.8 50.0 1.0
SG B:CYS19 4.8 43.1 1.0
CB B:CYS19 4.9 41.1 1.0
CG B:PRO11 4.9 52.9 1.0
C B:CYS22 4.9 41.8 1.0
C B:PRO11 5.0 52.1 1.0

Iron binding site 7 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 7 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:48.7
occ:1.00
 FE2 B:SF4501 0.0 48.7 1.0
S4 B:SF4501 2.3 48.5 1.0
S1 B:SF4501 2.3 48.4 1.0
S3 B:SF4501 2.3 48.5 1.0
SG B:CYS19 2.3 43.1 1.0
FE3 B:SF4501 2.7 48.4 1.0
FE1 B:SF4501 2.8 47.9 1.0
FE4 B:SF4501 2.8 48.2 1.0
CB B:CYS19 3.1 41.1 1.0
O B:HOH649 3.6 56.3 1.0
N B:CYS19 3.8 41.3 1.0
S2 B:SF4501 3.9 48.8 1.0
NZ B:LYS119 3.9 48.5 1.0
CA B:CYS19 4.1 41.1 1.0
OH B:TYR115 4.1 42.1 1.0
CE B:LYS119 4.3 47.3 1.0
CB B:CYS22 4.5 39.8 1.0
SG B:CYS22 4.6 40.5 1.0
SG B:CYS15 4.9 50.0 1.0
CB B:CYS15 4.9 46.3 1.0
C B:PHE18 5.0 42.2 1.0

Iron binding site 8 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 8 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:48.4
occ:1.00
 FE3 B:SF4501 0.0 48.4 1.0
OH B:TYR115 1.7 42.1 1.0
S1 B:SF4501 2.3 48.4 1.0
S2 B:SF4501 2.3 48.8 1.0
S4 B:SF4501 2.3 48.5 1.0
FE4 B:SF4501 2.7 48.2 1.0
FE2 B:SF4501 2.7 48.7 1.0
CZ B:TYR115 2.8 41.9 1.0
FE1 B:SF4501 2.8 47.9 1.0
CE2 B:TYR115 3.2 41.3 1.0
O B:HOH649 3.5 56.3 1.0
O2' B:MTA503 3.8 48.7 1.0
S3 B:SF4501 3.9 48.5 1.0
CE1 B:TYR115 4.0 41.4 1.0
C2' B:MTA503 4.4 48.8 1.0
OG B:SER117 4.5 47.4 1.0
CD2 B:TYR115 4.5 40.7 1.0
O B:HOH676 4.6 48.6 1.0
SG B:CYS15 4.8 50.0 1.0
SG B:CYS19 4.8 43.1 1.0
SG B:CYS22 4.9 40.5 1.0

Iron binding site 9 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 9 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:48.2
occ:1.00
 FE4 B:SF4501 0.0 48.2 1.0
S2 B:SF4501 2.3 48.8 1.0
S1 B:SF4501 2.3 48.4 1.0
SG B:CYS15 2.3 50.0 1.0
S3 B:SF4501 2.3 48.5 1.0
FE3 B:SF4501 2.7 48.4 1.0
FE1 B:SF4501 2.8 47.9 1.0
FE2 B:SF4501 2.8 48.7 1.0
CB B:CYS15 3.2 46.3 1.0
N B:GLY12 3.9 51.6 1.0
S4 B:SF4501 3.9 48.5 1.0
OH B:TYR115 4.2 42.1 1.0
CA B:PRO11 4.3 52.5 1.0
N B:ASP90 4.3 46.6 1.0
CE2 B:TYR115 4.5 41.3 1.0
CB B:PRO11 4.5 52.7 1.0
CA B:CYS15 4.6 45.7 1.0
C B:PRO11 4.6 52.1 1.0
NZ B:LYS119 4.7 48.5 1.0
CA B:GLY12 4.7 51.6 1.0
CA B:GLY89 4.8 49.1 1.0
SG B:CYS22 4.8 40.5 1.0
CZ B:TYR115 4.8 41.9 1.0
SG B:CYS19 4.8 43.1 1.0
CB B:ASP90 4.9 45.7 1.0
CE B:LYS119 4.9 47.3 1.0

Iron binding site 10 out of 10 in 7qbu

Go back to Iron Binding Sites List in 7qbu
Iron binding site 10 out of 10 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:45.3
occ:1.00
 SG B:CYS48 2.2 51.3 1.0
SG B:CYS38 2.3 59.0 1.0
SG B:CYS35 2.4 45.5 1.0
SG B:CYS45 2.4 53.7 1.0
CB B:CYS48 3.1 54.5 1.0
CB B:CYS35 3.4 45.2 1.0
CB B:CYS45 3.5 54.0 1.0
N B:CYS35 3.5 45.8 1.0
N B:CYS45 3.6 55.7 1.0
N B:CYS48 3.6 54.4 1.0
CB B:CYS38 3.7 55.6 1.0
N B:CYS38 3.8 53.0 1.0
CA B:CYS35 4.0 45.2 1.0
CA B:CYS38 4.0 55.2 1.0
CA B:CYS45 4.0 54.7 1.0
CA B:CYS48 4.0 55.5 1.0
C B:GLY34 4.1 47.3 1.0
C B:GLY44 4.2 56.6 1.0
CA B:GLY34 4.4 49.7 1.0
C B:TYR37 4.5 51.5 1.0
CA B:GLY44 4.5 57.3 1.0
C B:CYS35 4.5 44.6 1.0
C B:CYS45 4.5 53.9 1.0
O B:CYS45 4.6 53.8 1.0
O B:CYS35 4.6 45.2 1.0
N B:GLY34 4.6 51.0 1.0
N B:GLY44 4.7 57.7 1.0
C B:TYR47 4.7 53.8 1.0
CB B:TYR47 4.8 51.0 1.0
O B:GLY34 4.8 46.6 1.0
CB B:TYR37 4.8 47.2 1.0
N B:TYR37 4.8 47.0 1.0
O B:GLY44 4.9 56.8 1.0
CA B:TYR37 4.9 48.3 1.0
N B:TYR47 5.0 52.4 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 18:10:40 2024

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