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Iron in PDB 6qkj: Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine

Protein crystallography data

The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj was solved by A.R.Stampfli, B.N.Badri, T.Schirmer, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 108.143, 201.288, 108.332, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.8

Other elements in 6qkj:

The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine (pdb code 6qkj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qkj

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Iron binding site 1 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.8
occ:1.00
NE2 A:HIS153 2.1 23.1 1.0
NE2 A:HIS157 2.1 22.8 1.0
NE2 A:HIS62 2.1 20.5 1.0
NAT A:AVJ502 2.1 24.4 1.0
CL A:CL503 2.5 57.4 1.0
CL A:CL504 2.5 44.4 1.0
CE1 A:HIS153 3.0 23.2 1.0
CE1 A:HIS157 3.0 23.4 1.0
CD2 A:HIS157 3.1 22.0 1.0
CE1 A:HIS62 3.1 21.7 1.0
CD2 A:HIS62 3.1 20.7 1.0
CD2 A:HIS153 3.1 23.5 1.0
CAM A:AVJ502 3.1 24.2 1.0
CAZ A:AVJ502 3.2 24.9 1.0
ND1 A:HIS157 4.2 24.1 1.0
ND1 A:HIS62 4.2 20.6 1.0
CG A:HIS157 4.2 23.0 1.0
ND1 A:HIS153 4.2 21.5 1.0
CG A:HIS62 4.2 21.6 1.0
CG A:HIS153 4.2 22.8 1.0
CAY A:AVJ502 4.3 24.4 1.0
NAR A:AVJ502 4.3 25.4 1.0
OG A:SER92 4.5 27.9 0.5
CB A:SER92 4.6 30.8 0.5
CB A:SER92 4.6 33.8 0.5
OG A:SER92 4.8 34.5 0.5

Iron binding site 2 out of 4 in 6qkj

Go back to Iron Binding Sites List in 6qkj
Iron binding site 2 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe505

b:23.1
occ:1.00
OE2 A:GLU9 1.9 30.0 1.0
NE2 A:HIS25 2.1 28.8 1.0
OE2 A:GLU148 2.1 21.1 1.0
N3 A:IMD506 2.2 26.6 1.0
OE1 A:GLU148 2.6 23.7 1.0
C4 A:IMD506 2.6 26.9 1.0
CD A:GLU148 2.6 23.4 1.0
CD A:GLU9 2.7 33.9 1.0
OE1 A:GLU9 2.8 32.6 1.0
CD2 A:HIS25 3.0 27.6 1.0
CE1 A:HIS25 3.1 29.9 1.0
C2 A:IMD506 3.4 26.6 1.0
C5 A:IMD506 3.9 26.7 1.0
CG A:GLU9 4.1 36.0 1.0
ND1 A:HIS25 4.1 27.3 1.0
CG A:HIS25 4.1 28.5 1.0
CZ3 A:TRP22 4.2 27.3 1.0
CG A:GLU148 4.2 24.0 1.0
CH2 A:TRP22 4.2 28.5 1.0
N1 A:IMD506 4.2 26.8 1.0
O A:HOH690 4.2 30.8 1.0
CE1 A:HIS152 4.5 24.1 1.0
CD1 A:LEU151 4.7 26.8 1.0
O A:HOH611 4.7 41.4 1.0
CB A:GLU148 4.9 23.9 1.0
ND1 A:HIS152 5.0 28.3 1.0

Iron binding site 3 out of 4 in 6qkj

Go back to Iron Binding Sites List in 6qkj
Iron binding site 3 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:24.8
occ:1.00
NE2 B:HIS157 2.1 24.0 1.0
NE2 B:HIS153 2.1 30.6 1.0
NE2 B:HIS62 2.1 26.1 1.0
NAT B:AVJ502 2.1 29.0 1.0
CL B:CL504 2.5 56.5 1.0
CL B:CL503 2.7 63.0 1.0
CE1 B:HIS157 3.0 24.9 1.0
CD2 B:HIS157 3.1 24.8 1.0
CE1 B:HIS62 3.1 25.6 1.0
CE1 B:HIS153 3.1 31.8 1.0
CD2 B:HIS62 3.1 25.4 1.0
CD2 B:HIS153 3.1 30.6 1.0
CAZ B:AVJ502 3.1 28.8 1.0
CAM B:AVJ502 3.1 28.2 1.0
ND1 B:HIS157 4.1 26.0 1.0
ND1 B:HIS62 4.2 25.9 1.0
CG B:HIS157 4.2 25.6 1.0
ND1 B:HIS153 4.2 31.6 1.0
CG B:HIS62 4.2 26.0 1.0
CG B:HIS153 4.2 29.6 1.0
NAR B:AVJ502 4.2 29.9 1.0
CAY B:AVJ502 4.3 28.6 1.0
OG B:SER92 4.4 42.7 0.5
CB B:SER92 4.6 44.3 0.5
CB B:SER92 4.6 44.4 0.5
OG B:SER92 4.7 42.4 0.5

Iron binding site 4 out of 4 in 6qkj

Go back to Iron Binding Sites List in 6qkj
Iron binding site 4 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe505

b:47.6
occ:1.00
OE2 B:GLU148 2.1 59.5 1.0
NE2 B:HIS25 2.2 44.1 1.0
N3 B:IMD506 2.6 55.1 1.0
C4 B:IMD506 2.7 54.0 1.0
CD B:GLU148 2.8 50.5 1.0
OE1 B:GLU148 2.9 50.0 1.0
CD2 B:HIS25 2.9 42.5 1.0
CE1 B:HIS25 3.4 41.1 1.0
C2 B:IMD506 3.8 55.0 1.0
CZ3 B:TRP22 3.9 48.9 1.0
C5 B:IMD506 3.9 50.3 1.0
CH2 B:TRP22 4.0 46.3 1.0
CG B:HIS25 4.1 40.4 1.0
ND1 B:HIS25 4.3 40.0 1.0
CG B:GLU148 4.3 43.9 1.0
CE1 B:HIS152 4.4 29.3 1.0
N1 B:IMD506 4.4 52.7 1.0
CD1 B:LEU151 4.7 35.8 1.0
CE3 B:TRP22 4.9 47.3 1.0
CB B:GLU148 5.0 37.9 1.0
ND1 B:HIS152 5.0 29.5 1.0

Reference:

A.R.Stampfli, K.V.Goncharenko, M.Meury, B.N.Dubey, T.Schirmer, F.P.Seebeck. An Alternative Active Site Architecture For O2ACTIVATION in the Ergothioneine Biosynthetic Egtb From Chloracidobacterium Thermophilum. J.Am.Chem.Soc. V. 141 5275 2019.
ISSN: ESSN 1520-5126
PubMed: 30883103
DOI: 10.1021/JACS.8B13023
Page generated: Wed Aug 7 07:59:30 2024

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