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

Protein crystallography data

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv 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) 49.40 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 155.498, 163, 77.328, 90, 90, 90
R / Rfree (%) 21.4 / 23.5

Other elements in 7qbv:

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

Sodium (Na) 4 atoms
Cobalt (Co) 4 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. (pdb code 7qbv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 7qbv

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Iron binding site 1 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.3
occ:1.00
FE1 A:SF4501 0.0 43.3 1.0
SG A:CYS22 2.2 46.4 1.0
S2 A:SF4501 2.3 42.8 1.0
S4 A:SF4501 2.3 42.8 1.0
S3 A:SF4501 2.3 42.7 1.0
FE3 A:SF4501 2.8 42.3 1.0
FE2 A:SF4501 2.8 42.7 1.0
FE4 A:SF4501 2.8 42.7 1.0
CB A:CYS22 3.1 43.3 1.0
S1 A:SF4501 3.9 42.6 1.0
CB A:PRO11 4.1 49.2 1.0
OH A:TYR115 4.2 53.4 1.0
CA A:CYS22 4.2 42.7 1.0
N A:GLY12 4.6 46.0 1.0
CD1 A:PHE18 4.7 44.8 1.0
SG A:CYS15 4.8 44.3 1.0
SG A:CYS19 4.8 43.5 1.0
CA A:PRO11 4.8 48.2 1.0
N A:CYS19 4.9 42.2 1.0
CB A:CYS19 5.0 42.3 1.0

Iron binding site 2 out of 20 in 7qbv

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Iron binding site 2 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.7
occ:1.00
FE2 A:SF4501 0.0 42.7 1.0
SG A:CYS19 2.3 43.5 1.0
S3 A:SF4501 2.3 42.7 1.0
S1 A:SF4501 2.3 42.6 1.0
S4 A:SF4501 2.3 42.8 1.0
FE4 A:SF4501 2.8 42.7 1.0
FE1 A:SF4501 2.8 43.3 1.0
FE3 A:SF4501 2.8 42.3 1.0
CB A:CYS19 3.2 42.3 1.0
O A:HOH606 3.8 47.5 1.0
N A:CYS19 3.8 42.2 1.0
OH A:TYR115 3.9 53.4 1.0
S2 A:SF4501 3.9 42.8 1.0
NZ A:LYS119 4.0 59.3 1.0
CA A:CYS19 4.1 42.2 1.0
CE A:LYS119 4.3 57.4 1.0
CB A:CYS22 4.4 43.3 1.0
SG A:CYS22 4.5 46.4 1.0
SG A:CYS15 4.9 44.3 1.0
CB A:CYS15 4.9 43.0 1.0
OG A:SER117 4.9 49.4 1.0
C A:PHE18 4.9 42.7 1.0

Iron binding site 3 out of 20 in 7qbv

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Iron binding site 3 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.3
occ:1.00
FE3 A:SF4501 0.0 42.3 1.0
OH A:TYR115 1.6 53.4 1.0
S2 A:SF4501 2.3 42.8 1.0
S4 A:SF4501 2.3 42.8 1.0
S1 A:SF4501 2.3 42.6 1.0
CZ A:TYR115 2.6 52.2 1.0
FE1 A:SF4501 2.8 43.3 1.0
FE4 A:SF4501 2.8 42.7 1.0
FE2 A:SF4501 2.8 42.7 1.0
CE2 A:TYR115 3.0 51.2 1.0
O A:HOH606 3.4 47.5 1.0
CE1 A:TYR115 3.9 51.4 1.0
S3 A:SF4501 3.9 42.7 1.0
OG A:SER117 4.3 49.4 1.0
C5' A:SAH503 4.4 51.0 0.9
CD2 A:TYR115 4.4 50.1 1.0
CG A:SAH503 4.6 53.5 0.9
C3' A:SAH503 4.7 49.0 0.9
C2' A:SAH503 4.7 48.6 0.9
SG A:CYS15 4.7 44.3 1.0
SG A:CYS22 4.9 46.4 1.0
SG A:CYS19 4.9 43.5 1.0

Iron binding site 4 out of 20 in 7qbv

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Iron binding site 4 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.7
occ:1.00
FE4 A:SF4501 0.0 42.7 1.0
SG A:CYS15 2.3 44.3 1.0
S1 A:SF4501 2.3 42.6 1.0
S3 A:SF4501 2.3 42.7 1.0
S2 A:SF4501 2.3 42.8 1.0
FE2 A:SF4501 2.8 42.7 1.0
FE1 A:SF4501 2.8 43.3 1.0
FE3 A:SF4501 2.8 42.3 1.0
CB A:CYS15 3.1 43.0 1.0
N A:GLY12 3.8 46.0 1.0
S4 A:SF4501 3.9 42.8 1.0
OH A:TYR115 4.2 53.4 1.0
CA A:PRO11 4.3 48.2 1.0
N A:ASP90 4.5 50.2 1.0
CB A:PRO11 4.5 49.2 1.0
CA A:CYS15 4.5 43.0 1.0
CE2 A:TYR115 4.5 51.2 1.0
C A:PRO11 4.6 47.1 1.0
CA A:GLY12 4.6 45.8 1.0
NZ A:LYS119 4.7 59.3 1.0
SG A:CYS19 4.8 43.5 1.0
CE A:LYS119 4.8 57.4 1.0
CA A:GLY89 4.8 51.5 1.0
SG A:CYS22 4.8 46.4 1.0
CZ A:TYR115 4.9 52.2 1.0
CB A:ASP90 4.9 50.2 1.0
O A:GLY17 5.0 43.8 1.0

Iron binding site 5 out of 20 in 7qbv

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Iron binding site 5 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:42.8
occ:1.00
SG A:CYS35 2.3 57.0 1.0
SG A:CYS45 2.3 56.8 1.0
SG A:CYS38 2.3 54.6 1.0
SG A:CYS48 2.4 63.1 1.0
CB A:CYS48 3.3 59.8 1.0
CB A:CYS35 3.4 54.1 1.0
N A:CYS35 3.5 54.2 1.0
CB A:CYS45 3.5 55.8 1.0
N A:CYS38 3.5 52.5 1.0
CB A:CYS38 3.6 53.4 1.0
N A:CYS45 3.7 56.0 1.0
CA A:CYS38 3.7 53.3 1.0
CA A:CYS35 3.9 53.6 1.0
N A:CYS48 3.9 57.8 1.0
CA A:CYS45 4.1 55.9 1.0
C A:GLY34 4.1 55.1 1.0
CA A:CYS48 4.2 59.1 1.0
O A:CYS35 4.2 53.3 1.0
C A:TYR37 4.3 52.0 1.0
C A:CYS35 4.3 52.9 1.0
C A:GLY44 4.3 56.7 1.0
CA A:GLY34 4.4 56.2 1.0
CA A:GLY44 4.6 57.3 1.0
C A:CYS45 4.6 56.5 1.0
O A:CYS45 4.7 56.9 1.0
N A:TYR37 4.7 51.1 1.0
CB A:TYR47 4.8 55.3 1.0
N A:GLY34 4.8 57.0 1.0
CA A:TYR37 4.8 51.4 1.0
N A:GLY44 4.8 57.5 1.0
CB A:TYR37 4.8 50.9 1.0
O A:GLY34 4.9 55.0 1.0
C A:TYR47 4.9 56.8 1.0
O A:TYR37 5.0 51.9 1.0

Iron binding site 6 out of 20 in 7qbv

Go back to Iron Binding Sites List in 7qbv
Iron binding site 6 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.7
occ:1.00
FE1 B:SF4501 0.0 40.7 1.0
SG B:CYS22 2.2 43.0 1.0
S3 B:SF4501 2.3 40.6 1.0
S4 B:SF4501 2.3 40.6 1.0
S2 B:SF4501 2.3 40.5 1.0
FE2 B:SF4501 2.7 40.8 1.0
FE3 B:SF4501 2.8 40.6 1.0
FE4 B:SF4501 2.8 40.6 1.0
CB B:CYS22 3.0 41.6 1.0
S1 B:SF4501 3.9 40.6 1.0
CA B:CYS22 4.1 41.3 1.0
CB B:PRO11 4.2 42.5 1.0
OH B:TYR115 4.3 45.7 1.0
CD1 B:PHE18 4.6 40.6 1.0
N B:GLY12 4.6 40.2 1.0
N B:CYS19 4.7 39.5 1.0
SG B:CYS19 4.7 43.2 1.0
CB B:CYS19 4.7 40.2 1.0
SG B:CYS15 4.7 40.6 1.0
CA B:PRO11 4.9 41.7 1.0
CD2 B:PHE24 4.9 47.4 1.0
CE1 B:PHE18 5.0 41.1 1.0

Iron binding site 7 out of 20 in 7qbv

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Iron binding site 7 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.8
occ:1.00
FE2 B:SF4501 0.0 40.8 1.0
SG B:CYS19 2.3 43.2 1.0
S4 B:SF4501 2.3 40.6 1.0
S3 B:SF4501 2.3 40.6 1.0
S1 B:SF4501 2.3 40.6 1.0
FE1 B:SF4501 2.7 40.7 1.0
FE3 B:SF4501 2.8 40.6 1.0
FE4 B:SF4501 2.8 40.6 1.0
CB B:CYS19 3.2 40.2 1.0
N B:CYS19 3.8 39.5 1.0
NZ B:LYS119 3.8 55.3 1.0
S2 B:SF4501 3.9 40.5 1.0
O B:HOH605 3.9 36.2 1.0
OH B:TYR115 4.0 45.7 1.0
CA B:CYS19 4.1 39.8 1.0
CE B:LYS119 4.1 53.6 1.0
CB B:CYS22 4.4 41.6 1.0
SG B:CYS22 4.6 43.0 1.0
SG B:CYS15 4.8 40.6 1.0
CB B:CYS15 4.8 39.4 1.0
C B:PHE18 4.9 39.7 1.0
OG B:SER117 4.9 42.9 1.0

Iron binding site 8 out of 20 in 7qbv

Go back to Iron Binding Sites List in 7qbv
Iron binding site 8 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.6
occ:1.00
FE3 B:SF4501 0.0 40.6 1.0
OH B:TYR115 1.6 45.7 1.0
S1 B:SF4501 2.3 40.6 1.0
S2 B:SF4501 2.3 40.5 1.0
S4 B:SF4501 2.3 40.6 1.0
CZ B:TYR115 2.7 44.3 1.0
FE4 B:SF4501 2.8 40.6 1.0
FE1 B:SF4501 2.8 40.7 1.0
FE2 B:SF4501 2.8 40.8 1.0
O B:HOH605 3.2 36.2 1.0
CE2 B:TYR115 3.2 43.5 1.0
S3 B:SF4501 3.9 40.6 1.0
CE1 B:TYR115 3.9 43.2 1.0
OG B:SER117 4.3 42.9 1.0
C5' B:SAH503 4.3 49.7 0.9
C2' B:SAH503 4.5 48.1 0.9
CD2 B:TYR115 4.6 42.6 1.0
CG B:SAH503 4.6 51.4 0.9
C3' B:SAH503 4.7 48.7 0.9
SG B:CYS19 4.7 43.2 1.0
SG B:CYS22 4.8 43.0 1.0
SG B:CYS15 4.8 40.6 1.0

Iron binding site 9 out of 20 in 7qbv

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Iron binding site 9 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:40.6
occ:1.00
FE4 B:SF4501 0.0 40.6 1.0
SG B:CYS15 2.3 40.6 1.0
S1 B:SF4501 2.3 40.6 1.0
S2 B:SF4501 2.3 40.5 1.0
S3 B:SF4501 2.3 40.6 1.0
FE3 B:SF4501 2.8 40.6 1.0
FE1 B:SF4501 2.8 40.7 1.0
FE2 B:SF4501 2.8 40.8 1.0
CB B:CYS15 3.1 39.4 1.0
N B:GLY12 3.9 40.2 1.0
S4 B:SF4501 3.9 40.6 1.0
OH B:TYR115 4.1 45.7 1.0
N B:ASP90 4.4 43.8 1.0
CE2 B:TYR115 4.4 43.5 1.0
CA B:PRO11 4.4 41.7 1.0
CB B:PRO11 4.5 42.5 1.0
CA B:CYS15 4.6 39.6 1.0
C B:PRO11 4.7 41.5 1.0
NZ B:LYS119 4.7 55.3 1.0
CA B:GLY89 4.7 44.9 1.0
CZ B:TYR115 4.7 44.3 1.0
CA B:GLY12 4.7 40.0 1.0
CE B:LYS119 4.8 53.6 1.0
CB B:ASP90 4.8 44.1 1.0
SG B:CYS22 4.8 43.0 1.0
C B:GLY89 4.9 44.9 1.0
SG B:CYS19 4.9 43.2 1.0

Iron binding site 10 out of 20 in 7qbv

Go back to Iron Binding Sites List in 7qbv
Iron binding site 10 out of 20 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:47.3
occ:1.00
SG B:CYS38 2.2 52.9 1.0
SG B:CYS45 2.3 56.8 1.0
SG B:CYS35 2.3 53.3 1.0
SG B:CYS48 2.5 58.8 1.0
N B:CYS38 3.4 52.1 1.0
CB B:CYS38 3.4 52.1 1.0
CB B:CYS48 3.4 56.5 1.0
N B:CYS35 3.5 52.0 1.0
CB B:CYS45 3.5 54.7 1.0
CB B:CYS35 3.5 51.8 1.0
CA B:CYS38 3.6 52.2 1.0
N B:CYS45 3.8 54.9 1.0
CA B:CYS35 3.9 51.7 1.0
N B:CYS48 4.0 54.8 1.0
C B:TYR37 4.1 52.5 1.0
C B:GLY34 4.1 52.8 1.0
CA B:CYS45 4.2 54.8 1.0
O B:CYS35 4.2 52.2 1.0
C B:CYS35 4.3 51.8 1.0
CA B:CYS48 4.3 55.9 1.0
C B:GLY44 4.3 55.6 1.0
CA B:GLY34 4.5 53.6 1.0
N B:TYR37 4.6 51.5 1.0
CA B:GLY44 4.7 56.0 1.0
CA B:TYR37 4.7 52.1 1.0
C B:CYS45 4.7 55.3 1.0
O B:CYS45 4.8 55.5 1.0
CB B:TYR37 4.8 52.2 1.0
N B:GLY44 4.8 56.3 1.0
CB B:TYR47 4.8 53.3 1.0
N B:GLY34 4.8 54.3 1.0
O B:TYR37 4.8 53.0 1.0
O B:GLY34 4.9 53.0 1.0
C B:TYR47 5.0 54.3 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 18:12:47 2024

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