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

Iron in PDB 7qbt: 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: 7qbt 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) 44.71 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 156.064, 163.915, 77.805, 90, 90, 90
R / Rfree (%) 20.3 / 22.9

Other elements in 7qbt:

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) 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-Methyl-5'-Thioadenosine Bound. (pdb code 7qbt). 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-Methyl-5'-Thioadenosine Bound., PDB code: 7qbt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 1 out of 20 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:26.8
occ:1.00
FE1 A:SF4501 0.0 26.8 1.0
S4 A:SF4501 2.3 29.0 1.0
SG A:CYS22 2.3 26.2 1.0
S2 A:SF4501 2.4 27.8 1.0
S3 A:SF4501 2.4 27.9 1.0
FE2 A:SF4501 2.8 28.2 1.0
FE3 A:SF4501 2.8 29.1 1.0
FE4 A:SF4501 2.8 27.4 1.0
CB A:CYS22 3.0 26.3 1.0
S1 A:SF4501 4.0 29.3 1.0
CS A:MTA503 4.0 42.9 1.0
CA A:CYS22 4.1 27.0 1.0
CB A:PRO11 4.3 28.5 1.0
OH A:TYR115 4.4 35.0 1.0
S5' A:MTA503 4.5 43.3 1.0
N A:GLY12 4.7 27.1 1.0
CD1 A:PHE18 4.8 30.9 1.0
SG A:CYS19 4.8 29.1 1.0
N A:CYS19 4.8 29.8 1.0
SG A:CYS15 4.9 26.4 1.0
CB A:CYS19 4.9 29.0 1.0
CA A:PRO11 4.9 27.6 1.0

Iron binding site 2 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 2 out of 20 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:28.2
occ:1.00
FE2 A:SF4501 0.0 28.2 1.0
SG A:CYS19 2.2 29.1 1.0
S3 A:SF4501 2.3 27.9 1.0
S1 A:SF4501 2.3 29.3 1.0
S4 A:SF4501 2.3 29.0 1.0
FE3 A:SF4501 2.8 29.1 1.0
FE1 A:SF4501 2.8 26.8 1.0
FE4 A:SF4501 2.8 27.4 1.0
CB A:CYS19 3.2 29.0 1.0
N A:CYS19 3.8 29.8 1.0
O A:HOH736 3.9 59.0 1.0
S2 A:SF4501 3.9 27.8 1.0
NZ A:LYS119 4.0 38.1 1.0
CA A:CYS19 4.1 29.1 1.0
CE A:LYS119 4.2 38.3 1.0
OH A:TYR115 4.2 35.0 1.0
CB A:CYS22 4.4 26.3 1.0
SG A:CYS22 4.7 26.2 1.0
CB A:CYS15 4.9 25.8 1.0
C A:PHE18 4.9 30.3 1.0
SG A:CYS15 4.9 26.4 1.0

Iron binding site 3 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 3 out of 20 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:29.1
occ:1.00
FE3 A:SF4501 0.0 29.1 1.0
OH A:TYR115 1.8 35.0 1.0
S2 A:SF4501 2.3 27.8 1.0
S1 A:SF4501 2.3 29.3 1.0
S4 A:SF4501 2.3 29.0 1.0
FE4 A:SF4501 2.7 27.4 1.0
FE2 A:SF4501 2.8 28.2 1.0
FE1 A:SF4501 2.8 26.8 1.0
CZ A:TYR115 2.8 34.5 1.0
CE2 A:TYR115 3.2 33.2 1.0
O A:HOH736 3.4 59.0 1.0
S5' A:MTA503 3.7 43.3 1.0
S3 A:SF4501 3.9 27.9 1.0
CE1 A:TYR115 4.1 34.1 1.0
OG A:SER117 4.3 29.6 1.0
CS A:MTA503 4.4 42.9 1.0
C2' A:MTA503 4.5 36.2 1.0
CD2 A:TYR115 4.6 31.9 1.0
SG A:CYS19 4.7 29.1 1.0
O2' A:MTA503 4.8 38.2 1.0
SG A:CYS15 4.8 26.4 1.0
C3' A:MTA503 4.9 36.8 1.0
O A:HOH708 5.0 47.4 1.0
SG A:CYS22 5.0 26.2 1.0

Iron binding site 4 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 4 out of 20 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:27.4
occ:1.00
FE4 A:SF4501 0.0 27.4 1.0
S1 A:SF4501 2.3 29.3 1.0
SG A:CYS15 2.3 26.4 1.0
S2 A:SF4501 2.3 27.8 1.0
S3 A:SF4501 2.4 27.9 1.0
FE3 A:SF4501 2.7 29.1 1.0
FE2 A:SF4501 2.8 28.2 1.0
FE1 A:SF4501 2.8 26.8 1.0
CB A:CYS15 3.1 25.8 1.0
N A:GLY12 3.9 27.1 1.0
S4 A:SF4501 4.0 29.0 1.0
N A:ASP90 4.3 27.2 1.0
OH A:TYR115 4.3 35.0 1.0
CA A:PRO11 4.5 27.6 1.0
CA A:CYS15 4.6 28.0 1.0
CE2 A:TYR115 4.6 33.2 1.0
CA A:GLY89 4.7 30.6 1.0
CB A:ASP90 4.7 24.8 1.0
C A:PRO11 4.7 27.2 1.0
CB A:PRO11 4.7 28.5 1.0
CA A:GLY12 4.8 27.8 1.0
CE A:LYS119 4.8 38.3 1.0
SG A:CYS19 4.8 29.1 1.0
NZ A:LYS119 4.8 38.1 1.0
C A:GLY89 4.9 29.7 1.0
CZ A:TYR115 4.9 34.5 1.0
SG A:CYS22 5.0 26.2 1.0

Iron binding site 5 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 5 out of 20 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:32.5
occ:1.00
SG A:CYS35 2.3 32.3 1.0
SG A:CYS38 2.3 34.8 1.0
SG A:CYS45 2.3 38.5 1.0
SG A:CYS48 2.4 35.7 1.0
CB A:CYS48 3.4 35.8 1.0
CB A:CYS35 3.5 31.9 1.0
CB A:CYS45 3.5 38.5 1.0
N A:CYS35 3.5 32.3 1.0
N A:CYS38 3.5 33.8 1.0
CB A:CYS38 3.5 34.3 1.0
N A:CYS45 3.7 39.2 1.0
CA A:CYS38 3.7 34.3 1.0
CA A:CYS35 3.9 31.9 1.0
N A:CYS48 4.0 35.9 1.0
CA A:CYS45 4.1 39.2 1.0
C A:GLY34 4.1 33.9 1.0
O A:CYS35 4.1 31.9 1.0
C A:GLY44 4.2 39.7 1.0
C A:TYR37 4.2 34.9 1.0
CA A:CYS48 4.3 36.4 1.0
C A:CYS35 4.3 32.4 1.0
CA A:GLY34 4.4 35.2 1.0
CA A:GLY44 4.5 40.0 1.0
C A:CYS45 4.6 40.4 1.0
N A:TYR37 4.6 34.5 1.0
O A:CYS45 4.7 40.4 1.0
N A:GLY44 4.7 40.6 1.0
N A:GLY34 4.7 36.1 1.0
CA A:TYR37 4.8 34.8 1.0
CB A:TYR37 4.8 34.9 1.0
CB A:TYR47 4.8 35.2 1.0
O A:TYR37 4.9 35.6 1.0
O A:GLY44 4.9 39.9 1.0
O A:GLY34 4.9 33.4 1.0

Iron binding site 6 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 6 out of 20 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:29.3
occ:1.00
FE1 B:SF4501 0.0 29.3 1.0
SG B:CYS22 2.3 29.2 1.0
S2 B:SF4501 2.3 29.9 1.0
S4 B:SF4501 2.3 29.5 1.0
S3 B:SF4501 2.4 30.3 1.0
FE2 B:SF4501 2.8 29.4 1.0
FE3 B:SF4501 2.8 30.1 1.0
FE4 B:SF4501 2.8 29.3 1.0
CB B:CYS22 3.1 27.2 1.0
CS B:MTA503 3.9 44.3 1.0
S1 B:SF4501 4.0 30.6 1.0
CA B:CYS22 4.2 28.1 1.0
CB B:PRO11 4.3 32.9 1.0
OH B:TYR115 4.4 38.0 1.0
S5' B:MTA503 4.4 44.6 1.0
N B:GLY12 4.7 32.3 1.0
CD1 B:PHE18 4.7 33.4 1.0
SG B:CYS19 4.8 29.6 1.0
N B:CYS19 4.8 30.0 1.0
CA B:PRO11 4.9 32.3 1.0
SG B:CYS15 4.9 30.3 1.0
CB B:CYS19 4.9 29.4 1.0

Iron binding site 7 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 7 out of 20 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:29.4
occ:1.00
FE2 B:SF4501 0.0 29.4 1.0
SG B:CYS19 2.3 29.6 1.0
S3 B:SF4501 2.3 30.3 1.0
S1 B:SF4501 2.3 30.6 1.0
S4 B:SF4501 2.3 29.5 1.0
FE4 B:SF4501 2.8 29.3 1.0
FE3 B:SF4501 2.8 30.1 1.0
FE1 B:SF4501 2.8 29.3 1.0
CB B:CYS19 3.2 29.4 1.0
O B:HOH631 3.4 37.2 1.0
N B:CYS19 3.8 30.0 1.0
S2 B:SF4501 3.9 29.9 1.0
NZ B:LYS119 4.0 40.6 1.0
CA B:CYS19 4.1 29.0 1.0
OH B:TYR115 4.2 38.0 1.0
CE B:LYS119 4.3 39.8 1.0
CB B:CYS22 4.4 27.2 1.0
SG B:CYS22 4.7 29.2 1.0
CB B:CYS15 4.8 29.8 1.0
SG B:CYS15 4.9 30.3 1.0
C B:PHE18 4.9 30.9 1.0

Iron binding site 8 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 8 out of 20 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:30.1
occ:1.00
FE3 B:SF4501 0.0 30.1 1.0
OH B:TYR115 1.7 38.0 1.0
S2 B:SF4501 2.3 29.9 1.0
S4 B:SF4501 2.3 29.5 1.0
S1 B:SF4501 2.4 30.6 1.0
FE4 B:SF4501 2.8 29.3 1.0
FE2 B:SF4501 2.8 29.4 1.0
FE1 B:SF4501 2.8 29.3 1.0
CZ B:TYR115 2.8 36.4 1.0
CE2 B:TYR115 3.2 34.9 1.0
S5' B:MTA503 3.6 44.6 1.0
S3 B:SF4501 3.9 30.3 1.0
O B:HOH631 4.1 37.2 1.0
CE1 B:TYR115 4.1 36.1 1.0
CS B:MTA503 4.3 44.3 1.0
OG B:SER117 4.4 34.2 1.0
C2' B:MTA503 4.5 37.0 1.0
CD2 B:TYR115 4.6 34.2 1.0
O2' B:MTA503 4.7 37.6 1.0
O B:HOH613 4.7 61.1 1.0
C3' B:MTA503 4.8 37.9 1.0
SG B:CYS19 4.8 29.6 1.0
SG B:CYS15 4.8 30.3 1.0
SG B:CYS22 4.9 29.2 1.0

Iron binding site 9 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 9 out of 20 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:29.3
occ:1.00
FE4 B:SF4501 0.0 29.3 1.0
S1 B:SF4501 2.3 30.6 1.0
S3 B:SF4501 2.3 30.3 1.0
S2 B:SF4501 2.3 29.9 1.0
SG B:CYS15 2.3 30.3 1.0
FE3 B:SF4501 2.8 30.1 1.0
FE2 B:SF4501 2.8 29.4 1.0
FE1 B:SF4501 2.8 29.3 1.0
CB B:CYS15 3.1 29.8 1.0
N B:GLY12 3.9 32.3 1.0
S4 B:SF4501 4.0 29.5 1.0
OH B:TYR115 4.3 38.0 1.0
N B:ASP90 4.4 29.9 1.0
CA B:PRO11 4.4 32.3 1.0
CA B:CYS15 4.6 30.4 1.0
CE2 B:TYR115 4.6 34.9 1.0
C B:PRO11 4.7 32.6 1.0
CA B:GLY12 4.7 32.5 1.0
CB B:PRO11 4.7 32.9 1.0
CB B:ASP90 4.8 27.1 1.0
SG B:CYS19 4.8 29.6 1.0
NZ B:LYS119 4.8 40.6 1.0
CE B:LYS119 4.9 39.8 1.0
CA B:GLY89 4.9 33.6 1.0
SG B:CYS22 4.9 29.2 1.0
CZ B:TYR115 4.9 36.4 1.0

Iron binding site 10 out of 20 in 7qbt

Go back to Iron Binding Sites List in 7qbt
Iron binding site 10 out of 20 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:46.1
occ:1.00
SG B:CYS45 2.3 52.0 1.0
SG B:CYS38 2.3 51.1 1.0
SG B:CYS35 2.3 43.9 1.0
SG B:CYS48 2.3 50.4 1.0
CB B:CYS48 3.3 50.7 1.0
CB B:CYS45 3.4 54.3 1.0
CB B:CYS35 3.5 45.2 1.0
N B:CYS35 3.5 46.9 1.0
N B:CYS45 3.6 55.9 1.0
N B:CYS38 3.6 54.0 1.0
CB B:CYS38 3.7 54.4 1.0
CA B:CYS38 3.8 55.8 1.0
N B:CYS48 3.9 50.7 1.0
CA B:CYS35 4.0 46.4 1.0
CA B:CYS45 4.0 54.8 1.0
C B:GLY34 4.1 48.5 1.0
C B:GLY44 4.1 58.0 1.0
CA B:CYS48 4.2 51.1 1.0
O B:CYS35 4.3 48.3 1.0
C B:TYR37 4.3 53.1 1.0
C B:CYS35 4.4 47.7 1.0
CA B:GLY34 4.4 49.6 1.0
CA B:GLY44 4.5 60.1 1.0
C B:CYS45 4.5 54.5 1.0
O B:CYS45 4.5 53.8 1.0
N B:GLY44 4.7 62.0 1.0
N B:GLY34 4.7 50.3 1.0
N B:TYR37 4.7 50.8 1.0
CB B:TYR47 4.8 50.5 1.0
CA B:TYR37 4.8 51.1 1.0
CB B:TYR37 4.9 50.1 1.0
C B:TYR47 4.9 51.0 1.0
O B:GLY44 4.9 58.6 1.0
O B:GLY34 4.9 48.5 1.0
O B:TYR37 5.0 53.4 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 18:10:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy