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Zinc in PDB 3b4n: Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi

Enzymatic activity of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi

All present enzymatic activity of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi:
4.2.2.2;

Protein crystallography data

The structure of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi, PDB code: 3b4n was solved by C.Creze, S.Castang, E.Derivery, R.Haser, V.Shevchik, P.Gouet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.02 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.600, 70.700, 73.400, 90.00, 112.80, 90.00
R / Rfree (%) 17.5 / 19.8

Other elements in 3b4n:

The structure of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi (pdb code 3b4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi, PDB code: 3b4n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3b4n

Go back to Zinc Binding Sites List in 3b4n
Zinc binding site 1 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn711

b:11.6
occ:1.00
 O A:HOH1385 1.8 16.2 1.0
OD1 A:ASP195 1.9 12.5 1.0
O A:HOH1386 2.0 15.3 1.0
OD2 A:ASP173 2.0 13.4 1.0
CG A:ASP195 2.6 11.4 1.0
OD2 A:ASP195 2.6 15.1 1.0
CG A:ASP173 2.9 13.5 1.0
OD1 A:ASP173 3.1 12.8 1.0
ZN A:ZN716 3.4 32.3 1.0
OG1 A:THR198 3.8 10.5 1.0
O A:HOH1698 3.8 43.4 1.0
CB A:GLU194 3.9 14.7 1.0
CB A:ASP195 4.1 11.3 1.0
O A:HOH1134 4.1 26.0 1.0
CB A:ASP173 4.3 10.5 1.0
O A:HOH1006 4.3 12.3 1.0
NZ A:LYS224 4.4 19.4 1.0
N A:ASP195 4.5 10.8 1.0
O A:ASP173 4.6 11.2 1.0
C A:GLU194 4.7 10.9 1.0
CA A:ASP173 4.7 10.4 1.0
O A:HOH1096 4.8 27.1 1.0
CE A:LYS224 4.8 18.1 1.0
CG A:GLU194 4.9 20.2 1.0
CA A:ASP195 4.9 9.1 1.0
C A:ASP173 5.0 10.0 1.0
NE2 A:HIS176 5.0 14.0 1.0
CA A:GLU194 5.0 12.1 1.0

Zinc binding site 2 out of 6 in 3b4n

Go back to Zinc Binding Sites List in 3b4n
Zinc binding site 2 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn714

b:13.0
occ:1.00
 OD1 A:ASP178 2.0 13.7 1.0
O A:HOH1390 2.0 16.1 1.0
ND1 A:HIS176 2.1 13.5 1.0
CG A:ASP178 2.7 13.1 1.0
OD2 A:ASP178 2.8 11.5 1.0
CE1 A:HIS176 3.0 15.4 1.0
CG A:HIS176 3.1 12.0 1.0
CB A:HIS176 3.5 11.6 1.0
OD1 A:ASN200 4.1 13.6 1.0
O A:HOH1468 4.1 27.9 1.0
NE2 A:HIS176 4.2 14.0 1.0
CB A:ASP178 4.2 10.5 1.0
CD2 A:HIS176 4.2 12.4 1.0
O A:HOH1040 4.3 21.8 1.0
CG A:PRO152 4.5 16.8 1.0
CD1 A:ILE155 4.5 15.9 1.0
CG1 A:ILE155 4.6 12.9 1.0
CG2 A:ILE155 4.8 11.1 1.0
O A:HOH1457 4.9 39.5 1.0

Zinc binding site 3 out of 6 in 3b4n

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Zinc binding site 3 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn716

b:32.3
occ:1.00
 OD1 A:ASP173 1.8 12.8 1.0
NE2 A:HIS176 2.1 14.0 1.0
O A:HOH1385 2.4 16.2 1.0
CE1 A:HIS176 2.7 15.4 1.0
CG A:ASP173 2.9 13.5 1.0
CD2 A:HIS176 3.3 12.4 1.0
ZN A:ZN711 3.4 11.6 1.0
OD2 A:ASP173 3.5 13.4 1.0
OG1 A:THR198 3.5 10.5 1.0
O A:HOH1134 3.6 26.0 1.0
ND1 A:HIS176 3.9 13.5 1.0
O A:HOH1386 4.1 15.3 1.0
CB A:THR198 4.1 8.2 1.0
CB A:ASP173 4.1 10.5 1.0
CG2 A:THR198 4.2 9.8 1.0
CG A:HIS176 4.2 12.0 1.0
O A:ASP173 4.4 11.2 1.0
O A:HOH1006 4.6 12.3 1.0
OD2 A:ASP195 4.8 15.1 1.0

Zinc binding site 4 out of 6 in 3b4n

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Zinc binding site 4 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn712

b:10.6
occ:1.00
 OD1 B:ASP178 1.9 10.0 1.0
OD1 A:ASP148 2.0 12.1 1.0
O A:HOH1387 2.0 12.0 1.0
ND1 B:HIS176 2.0 10.2 1.0
CG B:ASP178 2.7 10.4 1.0
CG A:ASP148 2.7 16.4 1.0
OD2 B:ASP178 2.8 9.8 1.0
CE1 B:HIS176 2.9 12.2 1.0
OD2 A:ASP148 3.0 17.4 1.0
CG B:HIS176 3.1 9.8 1.0
CB B:HIS176 3.5 9.1 1.0
O B:HOH1222 3.8 27.0 1.0
NE2 B:HIS176 4.1 11.0 1.0
CB A:ASP148 4.1 15.1 1.0
O B:HOH1141 4.1 25.3 1.0
OD1 B:ASN200 4.1 12.6 1.0
CB B:ASP178 4.1 10.2 1.0
CD2 B:HIS176 4.2 9.4 1.0
O A:ASP146 4.3 13.2 1.0
O A:HOH1053 4.4 17.6 1.0
CG B:PRO152 4.4 12.8 1.0
CD1 B:ILE155 4.5 16.6 1.0
CG1 B:ILE155 4.5 11.4 1.0
CG2 B:ILE155 4.8 11.6 1.0
N A:ASP148 4.8 14.5 1.0

Zinc binding site 5 out of 6 in 3b4n

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Zinc binding site 5 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn713

b:10.0
occ:1.00
 O B:HOH1389 1.9 9.0 1.0
OD1 B:ASP195 2.0 11.0 1.0
O B:HOH1388 2.0 14.6 1.0
OD2 B:ASP173 2.0 11.1 1.0
OD2 B:ASP195 2.6 12.3 1.0
CG B:ASP195 2.6 10.9 1.0
CG B:ASP173 2.9 9.9 1.0
OD1 B:ASP173 3.2 9.6 1.0
ZN B:ZN715 3.2 11.2 1.0
OG1 B:THR198 3.8 9.0 1.0
O B:HOH1169 3.9 14.7 1.0
O A:HOH1350 4.0 17.2 1.0
CB B:GLU194 4.0 12.6 1.0
CB B:ASP195 4.1 10.6 1.0
O B:HOH1157 4.3 11.0 1.0
CG B:GLN227 4.3 16.3 1.0
OD1 A:ASP146 4.3 11.3 1.0
OE1 B:GLN227 4.3 18.8 1.0
CB B:ASP173 4.3 9.9 1.0
O B:HOH1620 4.4 34.1 1.0
O B:ASP173 4.4 9.3 1.0
O B:HOH1272 4.5 21.0 1.0
N B:ASP195 4.6 9.1 1.0
CD B:GLN227 4.7 18.0 1.0
CA B:ASP173 4.7 9.3 1.0
C B:GLU194 4.8 10.2 1.0
C B:ASP173 4.9 8.9 1.0
CG B:GLU194 4.9 18.4 1.0
NE2 B:HIS176 4.9 11.0 1.0
CG A:ASP146 4.9 13.9 1.0
CA B:ASP195 4.9 10.0 1.0

Zinc binding site 6 out of 6 in 3b4n

Go back to Zinc Binding Sites List in 3b4n
Zinc binding site 6 out of 6 in the Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of Pectate Lyase Peli From Erwinia Chrysanthemi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn715

b:11.2
occ:1.00
 O B:HOH1389 2.0 9.0 1.0
NE2 B:HIS176 2.0 11.0 1.0
OD1 B:ASP173 2.0 9.6 1.0
OD1 A:ASP146 2.0 11.3 1.0
OD2 A:ASP146 2.6 12.4 1.0
CG A:ASP146 2.6 13.9 1.0
CE1 B:HIS176 2.8 12.2 1.0
CG B:ASP173 3.0 9.9 1.0
CD2 B:HIS176 3.1 9.4 1.0
ZN B:ZN713 3.2 10.0 1.0
OD2 B:ASP173 3.4 11.1 1.0
OG1 B:THR198 3.7 9.0 1.0
O A:HOH1350 3.8 17.2 1.0
O B:HOH1169 3.9 14.7 1.0
ND1 B:HIS176 4.0 10.2 1.0
O B:HOH1388 4.0 14.6 1.0
O A:HOH1356 4.1 39.8 1.0
CB A:ASP146 4.1 14.3 1.0
CG B:HIS176 4.1 9.8 1.0
CB B:ASP173 4.2 9.9 1.0
CB B:THR198 4.2 7.5 1.0
O B:ASP173 4.3 9.3 1.0
CG2 B:THR198 4.3 8.3 1.0
O B:HOH1157 4.5 11.0 1.0
O A:ASP146 4.7 13.2 1.0
OD2 B:ASP195 4.7 12.3 1.0
CA A:ASP146 4.8 13.3 1.0
O B:HOH1272 4.9 21.0 1.0
OD1 B:ASN200 5.0 12.6 1.0

Reference:

C.Creze, S.Castang, E.Derivery, R.Haser, N.Hugouvieux-Cotte-Pattat, V.E.Shevchik, P.Gouet. The Crystal Structure of Pectate Lyase Peli From Soft Rot Pathogen Erwinia Chrysanthemi in Complex with Its Substrate. J.Biol.Chem. V. 283 18260 2008.
ISSN: ISSN 0021-9258
PubMed: 18430740
DOI: 10.1074/JBC.M709931200
Page generated: Wed Dec 16 04:08:30 2020

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