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Zinc in PDB 2i2x: Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri

Enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri

All present enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri:
2.1.1.90;

Protein crystallography data

The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x was solved by C.H.Hagemeier, M.Kruer, R.K.Thauer, E.Warkentin, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.750, 172.850, 190.540, 90.00, 98.86, 90.00
R / Rfree (%) 18.2 / 23.1

Other elements in 2i2x:

The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri also contains other interesting chemical elements:

Cobalt (Co) 8 atoms
Potassium (K) 8 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri (pdb code 2i2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 2i2x

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Zinc binding site 1 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.9
occ:1.00
 OE1 A:GLU164 2.1 22.3 1.0
SG A:CYS220 2.2 14.5 1.0
SG A:CYS269 2.4 14.2 1.0
K A:K511 2.9 23.5 0.7
CD A:GLU164 2.9 20.5 1.0
OE2 A:GLU164 2.9 24.6 1.0
CB A:CYS220 3.0 10.5 1.0
CB A:CYS269 3.4 10.0 1.0
OE1 A:GLU313 3.8 13.9 1.0
CG A:GLU164 4.3 15.3 1.0
ND2 A:ASN224 4.3 7.9 1.0
CA A:CYS220 4.4 10.9 1.0
O B:HOH501 4.5 42.7 1.0
CD A:GLU313 4.7 14.7 1.0
OE2 A:GLU313 4.8 13.8 1.0
CG2 A:THR218 4.8 5.5 1.0
CB A:GLU164 4.8 10.5 1.0
CA A:CYS269 4.8 9.6 1.0
OE2 A:GLU86 4.8 19.5 1.0

Zinc binding site 2 out of 12 in 2i2x

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Zinc binding site 2 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn524

b:9.0
occ:1.00
 OE2 A:GLU320 1.8 7.5 1.0
OE2 C:GLU320 1.8 10.9 1.0
NE2 A:HIS318 2.0 7.0 1.0
NE2 C:HIS318 2.0 8.7 1.0
CD A:GLU320 2.9 8.0 1.0
CD C:GLU320 2.9 10.0 1.0
CE1 A:HIS318 2.9 5.5 1.0
CE1 C:HIS318 3.0 6.8 1.0
CD2 A:HIS318 3.0 7.7 1.0
CD2 C:HIS318 3.1 8.9 1.0
OE1 C:GLU320 3.3 11.8 1.0
OE1 A:GLU320 3.3 9.9 1.0
ND1 A:HIS318 4.1 6.4 1.0
ND1 C:HIS318 4.1 9.4 1.0
CG A:GLU320 4.1 7.4 1.0
CG C:GLU320 4.1 9.5 1.0
CG A:HIS318 4.2 9.0 1.0
CG C:HIS318 4.2 10.4 1.0
O C:GLY319 4.4 8.0 1.0
O A:GLY319 4.6 8.4 1.0
OG1 C:THR325 4.6 11.6 1.0
O A:HOH666 4.8 13.3 1.0
OG1 A:THR325 5.0 12.8 1.0

Zinc binding site 3 out of 12 in 2i2x

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Zinc binding site 3 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:19.9
occ:1.00
 OE1 C:GLU164 2.2 18.0 1.0
SG C:CYS220 2.3 10.5 1.0
SG C:CYS269 2.4 14.3 1.0
CB C:CYS220 2.8 9.8 1.0
K C:K512 3.0 22.0 0.7
CD C:GLU164 3.0 15.8 1.0
OE2 C:GLU164 3.1 17.9 1.0
CB C:CYS269 3.4 10.6 1.0
OE1 C:GLU313 4.0 15.3 1.0
ND2 C:ASN224 4.2 8.2 1.0
CA C:CYS220 4.3 9.6 1.0
CG C:GLU164 4.4 13.6 1.0
O D:HOH501 4.6 20.5 1.0
OE2 C:GLU313 4.7 16.9 1.0
CG2 C:THR218 4.7 3.2 1.0
CD C:GLU313 4.8 13.5 1.0
CA C:CYS269 4.8 9.5 1.0
OE2 C:GLU86 4.8 22.1 1.0
CB C:GLU164 4.8 10.6 1.0

Zinc binding site 4 out of 12 in 2i2x

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Zinc binding site 4 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:37.0
occ:0.70
 OE1 E:GLU164 2.3 38.0 1.0
SG E:CYS269 2.3 36.4 1.0
SG E:CYS220 2.3 35.1 1.0
CD E:GLU164 2.7 36.3 1.0
OE2 E:GLU164 2.9 38.4 1.0
K E:K513 3.0 33.9 0.7
CB E:CYS220 3.1 32.4 1.0
CB E:CYS269 3.3 32.8 1.0
OE1 E:GLU313 3.7 37.9 1.0
CG E:GLU164 3.9 34.0 1.0
ND2 E:ASN224 4.3 29.3 1.0
CA E:CYS220 4.5 32.4 1.0
OE2 E:GLU313 4.5 38.0 1.0
CD E:GLU313 4.6 37.1 1.0
CG2 E:THR218 4.7 29.3 1.0
O F:HOH501 4.7 17.7 0.5
CA E:CYS269 4.8 32.9 1.0
CB E:GLU164 4.8 32.4 1.0
OG1 E:THR218 5.0 31.8 1.0
CB E:THR218 5.0 30.4 1.0

Zinc binding site 5 out of 12 in 2i2x

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Zinc binding site 5 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn522

b:37.1
occ:1.00
 OE2 E:GLU320 1.7 29.2 1.0
OE2 G:GLU320 1.7 27.2 1.0
NE2 G:HIS318 2.0 25.7 1.0
NE2 E:HIS318 2.2 32.8 1.0
CD G:GLU320 2.7 28.4 1.0
CD E:GLU320 2.8 30.1 1.0
CD2 E:HIS318 3.0 32.5 1.0
CE1 G:HIS318 3.0 26.1 1.0
CD2 G:HIS318 3.1 25.8 1.0
OE1 G:GLU320 3.2 29.4 1.0
CE1 E:HIS318 3.3 30.8 1.0
OE1 E:GLU320 3.3 29.1 1.0
CG E:GLU320 4.0 30.2 1.0
CG G:GLU320 4.0 27.1 1.0
ND1 G:HIS318 4.1 26.5 1.0
CG G:HIS318 4.2 27.0 1.0
CG E:HIS318 4.2 32.2 1.0
ND1 E:HIS318 4.3 31.8 1.0
O G:GLY319 4.5 28.4 1.0
O E:GLY319 4.5 31.4 1.0
OG1 E:THR325 4.6 33.9 1.0
OG1 G:THR325 4.9 27.1 1.0

Zinc binding site 6 out of 12 in 2i2x

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Zinc binding site 6 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn504

b:33.2
occ:0.70
 SG G:CYS220 2.0 28.3 1.0
SG G:CYS269 2.2 28.3 1.0
OE1 G:GLU164 2.2 34.5 1.0
CD G:GLU164 2.8 33.3 1.0
OE2 G:GLU164 3.0 34.1 1.0
K G:K514 3.0 40.0 0.7
CB G:CYS220 3.0 28.3 1.0
CB G:CYS269 3.2 25.4 1.0
OE1 G:GLU313 3.7 30.7 1.0
ND2 G:ASN224 4.0 30.9 1.0
CG G:GLU164 4.1 32.3 1.0
CA G:CYS220 4.4 28.3 1.0
O H:HOH501 4.5 18.1 0.5
CD G:GLU313 4.5 30.3 1.0
CG2 G:THR218 4.6 25.9 1.0
OE2 G:GLU313 4.6 32.8 1.0
CA G:CYS269 4.6 25.7 1.0
OE2 G:GLU86 4.8 33.7 1.0
CB G:GLU164 4.9 30.7 1.0

Zinc binding site 7 out of 12 in 2i2x

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Zinc binding site 7 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn505

b:30.0
occ:1.00
 OE1 I:GLU164 2.3 28.1 1.0
SG I:CYS220 2.3 21.9 1.0
SG I:CYS269 2.4 18.5 1.0
CB I:CYS220 2.9 20.1 1.0
CD I:GLU164 2.9 25.1 1.0
OE2 I:GLU164 3.0 25.7 1.0
K I:K515 3.0 28.7 0.7
CB I:CYS269 3.4 15.0 1.0
OE1 I:GLU313 4.1 23.1 1.0
CG I:GLU164 4.3 22.1 1.0
CA I:CYS220 4.3 20.3 1.0
ND2 I:ASN224 4.3 19.8 1.0
CG2 I:THR218 4.6 15.3 1.0
OE2 I:GLU313 4.7 22.1 1.0
CA I:CYS269 4.8 15.6 1.0
CD I:GLU313 4.8 20.6 1.0
CB I:GLU164 4.9 19.8 1.0
OG1 I:THR218 4.9 20.9 1.0
CB I:THR218 4.9 17.5 1.0

Zinc binding site 8 out of 12 in 2i2x

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Zinc binding site 8 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn521

b:16.4
occ:1.00
 OE2 I:GLU320 1.8 15.9 1.0
OE2 K:GLU320 1.9 9.1 1.0
NE2 K:HIS318 2.1 15.4 1.0
NE2 I:HIS318 2.1 11.6 1.0
CD K:GLU320 2.9 12.8 1.0
CD I:GLU320 2.9 18.2 1.0
CD2 K:HIS318 3.0 15.0 1.0
CE1 K:HIS318 3.1 14.3 1.0
CD2 I:HIS318 3.1 12.0 1.0
CE1 I:HIS318 3.1 10.7 1.0
OE1 K:GLU320 3.3 12.1 1.0
OE1 I:GLU320 3.4 18.5 1.0
CG K:HIS318 4.2 16.8 1.0
ND1 K:HIS318 4.2 16.4 1.0
CG I:GLU320 4.2 16.5 1.0
ND1 I:HIS318 4.2 10.0 1.0
CG I:HIS318 4.2 13.9 1.0
CG K:GLU320 4.3 14.1 1.0
O I:GLY319 4.4 18.7 1.0
O K:GLY319 4.5 16.5 1.0
OG1 I:THR325 4.6 19.4 1.0
OG1 K:THR325 4.7 18.9 1.0

Zinc binding site 9 out of 12 in 2i2x

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Zinc binding site 9 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn506

b:33.5
occ:1.00
 SG K:CYS220 2.1 24.5 1.0
OE1 K:GLU164 2.3 33.9 1.0
SG K:CYS269 2.5 24.8 1.0
CB K:CYS220 2.9 20.9 1.0
CD K:GLU164 2.9 29.8 1.0
OE2 K:GLU164 3.0 30.9 1.0
K K:K516 3.0 31.9 0.7
CB K:CYS269 3.6 19.6 1.0
OE1 K:GLU313 3.9 20.8 1.0
CA K:CYS220 4.3 20.8 1.0
CG K:GLU164 4.3 25.1 1.0
ND2 K:ASN224 4.4 21.5 1.0
CG2 K:THR218 4.7 17.1 1.0
OE2 K:GLU313 4.7 19.6 1.0
CD K:GLU313 4.7 18.8 1.0
CB K:GLU164 4.8 22.3 1.0
O L:HOH501 4.9 18.9 0.5
NZ K:LYS267 4.9 20.8 1.0
CA K:CYS269 5.0 19.3 1.0

Zinc binding site 10 out of 12 in 2i2x

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Zinc binding site 10 out of 12 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn507

b:33.9
occ:1.00
 OE1 M:GLU164 2.3 32.0 1.0
SG M:CYS220 2.3 23.4 1.0
SG M:CYS269 2.5 22.7 1.0
CB M:CYS220 2.9 21.7 1.0
CD M:GLU164 3.0 28.2 1.0
K M:K517 3.0 33.7 0.7
OE2 M:GLU164 3.1 29.0 1.0
CB M:CYS269 3.4 19.1 1.0
O M:HOH615 3.4 27.2 1.0
OE1 M:GLU313 4.0 22.9 1.0
ND2 M:ASN224 4.2 20.3 1.0
CG M:GLU164 4.3 24.6 1.0
CA M:CYS220 4.3 21.5 1.0
CG2 M:THR218 4.7 16.9 1.0
OE2 M:GLU313 4.7 23.2 1.0
CD M:GLU313 4.8 21.6 1.0
CA M:CYS269 4.8 18.4 1.0
OG1 M:THR218 4.9 21.9 1.0
CB M:GLU164 4.9 22.3 1.0
O N:HOH501 4.9 10.9 0.5
CB M:THR218 4.9 18.7 1.0

Reference:

C.H.Hagemeier, M.Krer, R.K.Thauer, E.Warkentin, U.Ermler. Insight Into the Mechanism of Biological Methanol Activation Based on the Crystal Structure of the Methanol-Cobalamin Methyltransferase Complex Proc.Natl.Acad.Sci.Usa V. 103 18917 2006.
ISSN: ISSN 0027-8424
PubMed: 17142327
DOI: 10.1073/PNAS.0603650103
Page generated: Thu Oct 17 00:47:40 2024

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