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Zinc in PDB 4r9g: CPMNBP1 with Mannotriose Bound

Protein crystallography data

The structure of CPMNBP1 with Mannotriose Bound, PDB code: 4r9g was solved by J.R.Chekan, V.Agarwal, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.331, 101.744, 67.775, 90.00, 116.71, 90.00
R / Rfree (%) 20.1 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the CPMNBP1 with Mannotriose Bound (pdb code 4r9g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the CPMNBP1 with Mannotriose Bound, PDB code: 4r9g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4r9g

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Zinc binding site 1 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:48.7
occ:1.00
 OD2 B:ASP31 2.1 36.1 1.0
OD2 A:ASP31 2.2 37.5 1.0
O A:HOH644 2.7 54.5 1.0
O B:HOH702 2.8 43.8 1.0
CG B:ASP31 2.8 34.3 1.0
OD1 B:ASP31 2.8 35.1 1.0
CG A:ASP31 2.9 35.5 1.0
O B:HOH750 3.0 52.3 1.0
OD1 A:ASP31 3.0 36.1 1.0
O A:GLY27 3.9 31.0 1.0
O B:GLY27 4.0 35.9 1.0
O A:HOH738 4.0 42.7 1.0
C A:GLY27 4.3 31.8 1.0
CB B:ASP31 4.3 31.3 1.0
C B:GLY27 4.4 34.4 1.0
CB A:ASP31 4.4 32.8 1.0
CA A:GLY27 4.6 30.1 1.0
CA B:GLY27 4.7 32.7 1.0
N B:GLY27 4.9 30.9 1.0
N A:GLY27 5.0 26.6 1.0

Zinc binding site 2 out of 8 in 4r9g

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Zinc binding site 2 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:50.5
occ:1.00
 OD2 A:ASP89 2.1 37.5 1.0
ND1 A:HIS195 2.1 28.2 1.0
OE2 A:GLU387 2.1 31.2 1.0
O A:HOH625 2.4 30.3 1.0
CD A:GLU387 2.9 29.5 1.0
CG A:ASP89 3.0 33.9 1.0
CE1 A:HIS195 3.0 28.6 1.0
CG A:HIS195 3.1 28.6 1.0
OE1 A:GLU387 3.1 30.7 1.0
CB A:ASP89 3.3 32.6 1.0
CB A:HIS195 3.5 26.0 1.0
O A:HOH753 4.1 41.7 1.0
OD1 A:ASP89 4.1 36.6 1.0
NE2 A:HIS195 4.1 31.0 1.0
CG A:GLU387 4.2 28.7 1.0
CD2 A:HIS195 4.2 29.7 1.0
O A:HOH726 4.3 41.6 1.0
O A:HOH713 4.4 37.8 1.0
CG A:MET383 4.8 39.6 1.0
CA A:ASP89 4.8 33.0 1.0
CA A:HIS195 4.9 26.8 1.0

Zinc binding site 3 out of 8 in 4r9g

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Zinc binding site 3 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:51.5
occ:1.00
 O A:HOH772 1.9 55.6 1.0
NE2 A:HIS44 2.3 36.3 1.0
O A:HOH640 2.3 31.9 1.0
O A:HOH733 2.9 35.4 1.0
CD2 A:HIS44 3.0 34.2 1.0
O A:HOH778 3.0 43.3 1.0
CE1 A:HIS44 3.4 36.4 1.0
OH A:TYR40 4.0 25.6 1.0
CE2 A:TYR40 4.2 25.8 1.0
CG A:HIS44 4.3 34.7 1.0
ND1 A:HIS44 4.4 35.4 1.0
CZ A:TYR40 4.5 27.3 1.0
CB A:ASP323 4.6 35.6 1.0
O A:HOH745 4.7 28.6 1.0
O A:ASP323 4.7 28.6 1.0

Zinc binding site 4 out of 8 in 4r9g

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Zinc binding site 4 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:37.8
occ:1.00
 ND1 A:HIS317 2.1 28.3 1.0
OE1 A:GLU320 2.1 36.9 1.0
O A:HOH601 2.3 8.8 1.0
CD A:GLU320 2.9 36.5 1.0
CE1 A:HIS317 3.0 26.3 1.0
OE2 A:GLU320 3.0 43.9 1.0
CG A:HIS317 3.1 29.2 1.0
CB A:HIS317 3.4 28.0 1.0
CA A:HIS317 3.9 29.9 1.0
NE2 A:HIS317 4.1 27.3 1.0
CD2 A:HIS317 4.2 28.2 1.0
CB A:GLN319 4.2 34.0 1.0
CG A:GLU320 4.3 34.4 1.0
C A:HIS317 4.4 27.8 1.0
N A:GLU320 4.4 28.8 1.0
O A:HOH716 4.5 53.8 1.0
N A:GLN319 4.6 31.1 1.0
O A:HIS317 4.7 27.1 1.0
O A:LYS316 4.8 36.6 1.0
CB A:GLU320 4.8 31.9 1.0
CA A:GLN319 4.9 30.3 1.0
N A:PRO318 4.9 26.4 1.0

Zinc binding site 5 out of 8 in 4r9g

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Zinc binding site 5 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:80.4
occ:1.00
 NE2 B:HIS44 2.4 50.8 1.0
O B:HOH661 2.5 42.8 1.0
CD2 B:HIS44 3.1 48.3 1.0
CE1 B:HIS44 3.5 48.0 1.0
OH B:TYR40 3.9 28.9 1.0
OD2 B:ASP323 3.9 50.1 1.0
CE2 B:TYR40 4.1 27.8 1.0
CG B:HIS44 4.3 47.1 1.0
CZ B:TYR40 4.4 29.1 1.0
ND1 B:HIS44 4.5 44.5 1.0
O B:HOH665 4.8 47.8 1.0
CG B:ASP323 4.9 43.7 1.0

Zinc binding site 6 out of 8 in 4r9g

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Zinc binding site 6 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:41.6
occ:1.00
 ND1 B:HIS317 2.0 32.3 1.0
OE1 B:GLU320 2.1 39.6 1.0
CE1 B:HIS317 2.9 32.8 1.0
CG B:HIS317 3.0 33.5 1.0
CD B:GLU320 3.1 43.1 1.0
CB B:HIS317 3.4 32.4 1.0
OE2 B:GLU320 3.5 49.1 1.0
CA B:HIS317 3.8 32.0 1.0
NE2 B:HIS317 4.1 32.6 1.0
CD2 B:HIS317 4.1 33.0 1.0
CB B:GLN319 4.2 33.3 1.0
C B:HIS317 4.4 30.0 1.0
CG B:GLU320 4.5 40.1 1.0
N B:GLU320 4.5 30.9 1.0
N B:GLN319 4.6 30.0 1.0
O B:LYS316 4.7 36.3 1.0
O B:HIS317 4.7 28.9 1.0
CB B:GLU320 4.9 35.6 1.0
CA B:GLN319 4.9 31.5 1.0
N B:PRO318 5.0 29.5 1.0

Zinc binding site 7 out of 8 in 4r9g

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Zinc binding site 7 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:57.2
occ:1.00
 CB B:ASN156 3.6 38.2 1.0
CG B:PRO155 3.7 31.8 1.0
OD1 B:ASP154 3.7 39.0 1.0
CG B:ASN156 3.8 43.0 1.0
OD1 B:ASN156 3.9 46.6 1.0
OD2 B:ASP154 3.9 35.1 1.0
N B:ASN156 4.0 32.7 1.0
CD B:PRO155 4.1 30.9 1.0
CG B:ASP154 4.2 35.4 1.0
ND2 B:ASN156 4.5 46.1 1.0
CA B:ASN156 4.5 34.7 1.0
N B:PRO155 4.6 32.6 1.0
CB B:PRO155 4.7 30.2 1.0
C B:PRO155 4.8 32.4 1.0
CA B:PRO155 5.0 32.0 1.0

Zinc binding site 8 out of 8 in 4r9g

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Zinc binding site 8 out of 8 in the CPMNBP1 with Mannotriose Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of CPMNBP1 with Mannotriose Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:40.9
occ:1.00
 OE2 B:GLU387 2.0 26.2 1.0
OD2 B:ASP89 2.1 38.6 1.0
ND1 B:HIS195 2.1 24.8 1.0
O B:HOH627 2.4 30.9 1.0
CD B:GLU387 2.8 27.8 1.0
O B:HOH790 2.8 39.8 1.0
CG B:ASP89 2.9 34.6 1.0
CE1 B:HIS195 3.0 25.1 1.0
CG B:HIS195 3.1 24.1 1.0
OE1 B:GLU387 3.1 28.5 1.0
CB B:ASP89 3.2 32.3 1.0
CB B:HIS195 3.4 24.4 1.0
OD1 B:ASP89 4.1 36.5 1.0
NE2 B:HIS195 4.1 26.6 1.0
CD2 B:HIS195 4.1 25.1 1.0
CG B:GLU387 4.2 26.8 1.0
O B:HOH687 4.4 32.0 1.0
O B:HOH609 4.5 23.2 1.0
O B:HOH637 4.5 34.2 1.0
O B:HOH629 4.5 32.1 1.0
CG B:MET383 4.6 39.8 1.0
CA B:ASP89 4.7 33.5 1.0
CA B:HIS195 4.9 26.0 1.0
O B:HIS195 5.0 24.8 1.0

Reference:

J.R.Chekan, I.H.Kwon, V.Agarwal, D.Dodd, V.Revindran, R.I.Mackie, I.Cann, S.K.Nair. Structural and Biochemical Basis For Mannan Utilization By Caldanaerobius Polysaccharolyticus Strain Atcc Baa-17. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25342756
DOI: 10.1074/JBC.M114.579904
Page generated: Sun Oct 27 06:57:36 2024

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