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Zinc in PDB 6s6y: X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

Enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

All present enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran:
2.3.1.101;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y was solved by T.Wagner, J.L.Hemmann, S.Shima, J.Vorholt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.95 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.974, 130.322, 172.689, 84.97, 75.91, 82.09
R / Rfree (%) 22.1 / 25.1

Other elements in 6s6y:

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran also contains other interesting chemical elements:

Potassium (K) 9 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran (pdb code 6s6y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6s6y

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Zinc binding site 1 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:67.7
occ:1.00
 OQ1 A:KCX176 2.0 92.7 1.0
NE2 A:HIS59 2.3 65.4 1.0
CD2 A:HIS59 3.0 66.2 1.0
CX A:KCX176 3.2 82.0 1.0
ZN A:ZN605 3.2 70.1 1.0
CE1 A:HIS59 3.4 64.2 1.0
CA A:SER310 3.9 62.5 1.0
OQ2 A:KCX176 3.9 86.5 1.0
N A:LEU311 3.9 53.8 1.0
O A:ILE309 3.9 52.5 1.0
NZ A:KCX176 3.9 65.5 1.0
CB A:ALA113 4.0 78.9 1.0
CG A:HIS59 4.3 63.9 1.0
OG A:SER310 4.3 74.5 1.0
C A:SER310 4.4 60.0 1.0
N1 A:MFN602 4.4 46.3 0.5
ND1 A:HIS59 4.4 64.8 1.0
CD1 A:ILE178 4.5 63.9 1.0
CB A:SER310 4.5 66.7 1.0
C A:ILE309 4.7 52.3 1.0
CD1 A:LEU311 4.7 55.8 1.0
N A:SER310 4.7 56.5 1.0
NE2 A:HIS57 4.8 0.1 1.0
CB A:LEU311 4.9 58.6 1.0
CG1 A:ILE178 5.0 63.0 1.0
CG A:PRO112 5.0 60.2 1.0

Zinc binding site 2 out of 8 in 6s6y

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Zinc binding site 2 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:70.1
occ:1.00
 OQ2 A:KCX176 2.3 86.5 1.0
OQ1 A:KCX176 2.3 92.7 1.0
NE2 A:HIS258 2.4 55.4 1.0
N1 A:MFN602 2.5 46.3 0.5
ND1 A:HIS229 2.6 90.7 1.0
CX A:KCX176 2.7 82.0 1.0
CE1 A:HIS229 2.9 90.3 1.0
ZN A:ZN604 3.2 67.7 1.0
CE1 A:HIS258 3.3 58.9 1.0
CD2 A:HIS258 3.4 57.2 1.0
C1 A:MFN602 3.5 47.4 0.5
OG A:SER310 3.7 74.5 1.0
CG A:HIS229 4.0 90.9 1.0
NZ A:KCX176 4.1 65.5 1.0
NE2 A:HIS59 4.2 65.4 1.0
NE2 A:HIS57 4.3 0.1 1.0
NE2 A:HIS229 4.3 90.0 1.0
ND1 A:HIS258 4.4 60.4 1.0
CE1 A:HIS59 4.5 64.2 1.0
CE1 A:HIS57 4.5 0.1 1.0
CG A:HIS258 4.5 59.1 1.0
CB A:SER310 4.6 66.7 1.0
CG2 A:ILE178 4.6 70.9 1.0
CB A:HIS229 4.7 93.7 1.0
CD2 A:HIS229 4.8 89.8 1.0
OD1 A:ASP377 4.8 73.3 1.0
C2 A:MFN602 4.8 48.4 0.5
ND2 A:ASN380 4.8 66.6 1.0
CE A:KCX176 5.0 63.6 1.0
CG1 A:ILE178 5.0 63.0 1.0
CA A:SER310 5.0 62.5 1.0

Zinc binding site 3 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 3 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:0.3
occ:1.00
 NE2 E:HIS258 2.4 0.8 1.0
OQ2 E:KCX176 2.9 0.3 1.0
OQ1 E:KCX176 3.0 0.1 1.0
CD2 E:HIS258 3.1 0.5 1.0
ND1 E:HIS229 3.1 0.7 1.0
CE1 E:HIS229 3.2 0.8 1.0
CE1 E:HIS258 3.3 0.7 1.0
CX E:KCX176 3.4 0.2 1.0
ZN E:ZN602 3.4 0.4 1.0
OG E:SER310 3.9 0.8 1.0
ND2 E:ASN380 4.0 0.2 1.0
NE2 E:HIS57 4.1 0.7 1.0
NE2 E:HIS59 4.1 0.5 1.0
OD1 E:ASP377 4.2 0.5 1.0
CG E:HIS258 4.2 0.5 1.0
CE1 E:HIS59 4.2 0.1 1.0
ND1 E:HIS258 4.3 0.5 1.0
OD2 E:ASP377 4.3 0.6 1.0
CB E:SER310 4.5 0.6 1.0
CE1 E:HIS57 4.5 0.5 1.0
CG E:HIS229 4.5 0.6 1.0
NE2 E:HIS229 4.5 0.0 1.0
CG E:ASP377 4.7 0.3 1.0
NZ E:KCX176 4.7 0.3 1.0
CD1 E:LEU233 4.7 0.3 1.0
O E:ILE309 4.9 0.1 1.0
CA E:SER310 5.0 0.9 1.0

Zinc binding site 4 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 4 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn602

b:0.4
occ:1.00
 OQ2 E:KCX176 2.0 0.3 1.0
NE2 E:HIS59 2.8 0.5 1.0
CX E:KCX176 3.0 0.2 1.0
ZN E:ZN601 3.4 0.3 1.0
CD2 E:HIS59 3.6 0.2 1.0
OQ1 E:KCX176 3.7 0.1 1.0
N E:LEU311 3.8 0.5 1.0
NZ E:KCX176 3.8 0.3 1.0
CA E:SER310 3.9 0.9 1.0
CE1 E:HIS59 3.9 0.1 1.0
CD1 E:ILE178 3.9 0.6 1.0
CB E:ALA113 4.1 0.3 1.0
O E:ILE309 4.1 0.1 1.0
OG E:SER310 4.1 0.8 1.0
CG1 E:ILE178 4.4 0.4 1.0
C E:SER310 4.4 1.0 1.0
CB E:SER310 4.4 0.6 1.0
CD1 E:LEU311 4.6 0.4 1.0
CB E:LEU311 4.8 0.3 1.0
CG E:HIS59 4.8 0.7 1.0
N E:SER310 4.8 0.4 1.0
C E:ILE309 4.9 95.6 1.0
ND1 E:HIS229 4.9 0.7 1.0
NE2 E:HIS57 4.9 0.7 1.0
CG2 E:ILE178 4.9 0.7 1.0
CA E:LEU311 4.9 0.4 1.0
ND1 E:HIS59 4.9 0.9 1.0

Zinc binding site 5 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 5 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn604

b:65.1
occ:1.00
 OQ2 I:KCX176 2.1 0.8 1.0
ND1 I:HIS229 2.4 57.0 1.0
NE2 I:HIS258 2.4 62.0 1.0
N1 I:L6K602 2.4 70.1 0.8
OQ1 I:KCX176 2.5 0.9 1.0
CX I:KCX176 2.7 0.1 1.0
CE1 I:HIS229 2.7 56.0 1.0
ZN I:ZN605 3.0 75.1 1.0
CD2 I:HIS258 3.3 65.6 1.0
CE1 I:HIS258 3.5 67.9 1.0
C1 I:L6K602 3.5 70.1 0.8
CG I:HIS229 3.7 59.3 1.0
NE2 I:HIS229 4.0 56.6 1.0
NZ I:KCX176 4.0 67.9 1.0
OG I:SER310 4.2 71.1 1.0
NE2 I:HIS57 4.3 79.5 1.0
NE2 I:HIS59 4.4 56.4 1.0
CB I:HIS229 4.4 64.5 1.0
CG I:HIS258 4.5 63.1 1.0
CD2 I:HIS229 4.5 58.2 1.0
ND1 I:HIS258 4.5 65.7 1.0
CE1 I:HIS57 4.5 81.7 1.0
CE1 I:HIS59 4.5 59.6 1.0
CG2 I:ILE178 4.7 76.5 1.0
ND2 I:ASN380 4.7 67.3 1.0
OD1 I:ASP377 4.8 67.9 1.0
C2 I:L6K602 4.8 70.1 0.8
OD2 I:ASP377 4.9 70.8 1.0
CE I:KCX176 4.9 54.8 1.0
CB I:SER310 4.9 65.6 1.0

Zinc binding site 6 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 6 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn605

b:75.1
occ:1.00
 OQ1 I:KCX176 2.0 0.9 1.0
NE2 I:HIS59 2.6 56.4 1.0
ZN I:ZN604 3.0 65.1 1.0
CX I:KCX176 3.1 0.1 1.0
CD2 I:HIS59 3.5 59.0 1.0
CE1 I:HIS59 3.6 59.6 1.0
OQ2 I:KCX176 3.6 0.8 1.0
CA I:SER310 3.8 69.3 1.0
O I:ILE309 3.8 69.4 1.0
N I:LEU311 3.9 63.4 1.0
NZ I:KCX176 4.0 67.9 1.0
N1 I:L6K602 4.0 70.1 0.8
OG I:SER310 4.1 71.1 1.0
CD1 I:ILE178 4.3 70.7 1.0
CB I:SER310 4.3 65.6 1.0
C I:SER310 4.4 69.4 1.0
CB I:ALA113 4.4 74.0 1.0
C I:ILE309 4.7 60.6 1.0
CG1 I:ILE178 4.7 72.9 1.0
CG I:HIS59 4.7 54.3 1.0
N I:SER310 4.7 63.0 1.0
ND1 I:HIS59 4.7 55.5 1.0
ND1 I:HIS229 4.8 57.0 1.0
NE2 I:HIS57 4.9 79.5 1.0
CG2 I:ILE178 4.9 76.5 1.0
ND2 I:ASN380 4.9 67.3 1.0
CE1 I:HIS229 5.0 56.0 1.0
CB I:LEU311 5.0 52.5 1.0
CD1 I:LEU311 5.0 52.8 1.0

Zinc binding site 7 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 7 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn601

b:85.1
occ:1.00
 OQ2 M:KCX176 2.2 0.2 1.0
NE2 M:HIS59 3.0 0.7 1.0
CX M:KCX176 3.2 0.8 1.0
ZN M:ZN602 3.3 80.1 1.0
N M:LEU311 3.3 0.2 1.0
CA M:SER310 3.5 1.0 1.0
OQ1 M:KCX176 3.6 0.1 1.0
OG M:SER310 3.7 0.9 1.0
CD2 M:HIS59 3.9 0.4 1.0
C M:SER310 3.9 0.4 1.0
CD1 M:ILE178 3.9 0.1 1.0
CE1 M:HIS59 3.9 0.5 1.0
O M:ILE309 4.0 0.2 1.0
CB M:SER310 4.0 0.2 1.0
NZ M:KCX176 4.1 0.2 1.0
CG1 M:ILE178 4.3 1.0 1.0
CB M:ALA113 4.4 0.5 1.0
CB M:LEU311 4.4 0.2 1.0
CA M:LEU311 4.5 0.2 1.0
N M:SER310 4.5 0.8 1.0
CG2 M:ILE178 4.5 0.7 1.0
ND1 M:HIS229 4.6 0.5 1.0
CD1 M:LEU311 4.6 0.9 1.0
C M:ILE309 4.7 0.6 1.0
CE1 M:HIS229 4.8 0.0 1.0

Zinc binding site 8 out of 8 in 6s6y

Go back to Zinc Binding Sites List in 6s6y
Zinc binding site 8 out of 8 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn602

b:80.1
occ:1.00
 NE2 M:HIS258 2.2 0.1 1.0
OQ1 M:KCX176 2.7 0.1 1.0
OQ2 M:KCX176 2.9 0.2 1.0
CD2 M:HIS258 2.9 0.4 1.0
ND1 M:HIS229 2.9 0.5 1.0
CE1 M:HIS229 3.1 0.0 1.0
CX M:KCX176 3.2 0.8 1.0
ZN M:ZN601 3.3 85.1 1.0
CE1 M:HIS258 3.3 0.2 1.0
NE2 M:HIS57 3.9 0.5 1.0
OG M:SER310 4.1 0.9 1.0
OD1 M:ASP377 4.1 0.7 1.0
CG M:HIS258 4.1 0.2 1.0
ND2 M:ASN380 4.2 0.7 1.0
CE1 M:HIS59 4.2 0.5 1.0
CE1 M:HIS57 4.2 0.6 1.0
OD2 M:ASP377 4.2 0.5 1.0
ND1 M:HIS258 4.2 0.1 1.0
CG M:HIS229 4.2 0.7 1.0
NE2 M:HIS59 4.3 0.7 1.0
NE2 M:HIS229 4.4 0.6 1.0
NZ M:KCX176 4.5 0.2 1.0
CG M:ASP377 4.6 0.2 1.0
CB M:SER310 4.7 0.2 1.0
CD1 M:LEU233 4.9 1.0 1.0
CB M:HIS229 5.0 0.3 1.0

Reference:

J.L.Hemmann, T.Wagner, S.Shima, J.Vorholt. Methylofuran Is A Prosthetic Group of the Formyltransferase/Hydrolase Complex and Shuttles One-Carbon Units Between Two Active Sites To Be Published.
Page generated: Tue Oct 29 07:02:07 2024

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