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Zinc in PDB 2cex: Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN

Protein crystallography data

The structure of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN, PDB code: 2cex was solved by A.Muller, E.Severi, C.Mulligan, A.G.Watts, D.J.Kelly, K.S.Wilson, A.J.Wilkinson, G.H.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.80 / 2.2
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.448, 88.701, 115.912, 90.00, 105.33, 90.00
R / Rfree (%) 19.7 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN (pdb code 2cex). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN, PDB code: 2cex:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2cex

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Zinc binding site 1 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1306

b:39.3
occ:0.50
OD2 A:ASP2 2.0 27.6 1.0
OD2 A:ASP4 2.1 38.6 1.0
OD1 A:ASP2 2.4 29.6 1.0
O A:HOH2088 2.4 38.8 1.0
OD1 A:ASP4 2.5 38.6 1.0
CG A:ASP2 2.5 31.6 1.0
CG A:ASP4 2.6 37.1 1.0
O A:HOH2089 3.3 43.0 1.0
O A:HOH2001 3.8 30.6 1.0
CB A:ASP2 4.0 33.4 1.0
CB A:ASP4 4.1 35.8 1.0
O A:ASP2 4.4 33.3 1.0
C A:ASP2 4.6 33.9 1.0
N A:ASP4 4.8 35.5 1.0
CA A:ASP4 4.8 35.7 1.0
CA A:ASP2 4.8 33.7 1.0

Zinc binding site 2 out of 6 in 2cex

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Zinc binding site 2 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1310

b:30.1
occ:1.00
O B:HOH2145 2.1 3.1 1.0
NE2 B:HIS269 2.2 33.0 1.0
O B:HOH2146 2.2 7.9 1.0
CE1 B:HIS269 3.2 32.4 1.0
CD2 B:HIS269 3.2 30.9 1.0
ND1 B:HIS269 4.3 32.0 1.0
CG B:HIS269 4.3 31.3 1.0
CG2 B:ILE267 4.9 28.0 1.0
CG1 B:VAL257 4.9 32.4 1.0

Zinc binding site 3 out of 6 in 2cex

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Zinc binding site 3 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1311

b:32.5
occ:0.50
OD2 B:ASP4 1.9 36.8 1.0
O B:HOH2147 2.1 31.5 1.0
OD2 B:ASP2 2.2 25.8 1.0
OD1 B:ASP2 2.3 25.1 1.0
CG B:ASP2 2.6 28.8 1.0
CG B:ASP4 2.9 34.6 1.0
OD1 B:ASP4 3.3 36.7 1.0
CB B:ASP2 4.2 30.9 1.0
CB B:ASP4 4.2 34.0 1.0
C B:ASP2 4.8 33.0 1.0
N B:ASP4 4.9 33.7 1.0
CA B:ASP2 5.0 31.9 1.0
O B:ASP2 5.0 33.4 1.0

Zinc binding site 4 out of 6 in 2cex

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Zinc binding site 4 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1306

b:30.9
occ:1.00
NE2 D:HIS269 2.0 27.9 1.0
NE2 C:HIS269 2.2 35.8 1.0
O C:HOH2096 2.2 2.8 1.0
O C:HOH2097 2.3 9.3 1.0
CE1 D:HIS269 2.9 28.4 1.0
CD2 D:HIS269 3.1 28.7 1.0
CE1 C:HIS269 3.2 34.8 1.0
CD2 C:HIS269 3.2 35.7 1.0
ND1 D:HIS269 4.0 28.2 1.0
O C:HOH2031 4.1 22.3 1.0
CG D:HIS269 4.1 31.7 1.0
O D:HOH2038 4.2 16.2 1.0
ND1 C:HIS269 4.3 34.9 1.0
CG C:HIS269 4.3 35.1 1.0
CG2 C:ILE267 4.5 32.7 1.0
O D:HOH2106 4.9 27.7 1.0

Zinc binding site 5 out of 6 in 2cex

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Zinc binding site 5 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1307

b:53.3
occ:0.50
OD2 C:ASP2 2.2 28.7 1.0
OD1 C:ASP2 2.6 27.6 1.0
CG C:ASP2 2.7 30.4 1.0
OD1 C:ASP4 2.8 33.1 1.0
OD2 C:ASP4 2.9 27.8 1.0
CG C:ASP4 3.2 33.0 1.0
CB C:ASP2 4.1 32.9 1.0
CB C:ASP4 4.7 33.2 1.0

Zinc binding site 6 out of 6 in 2cex

Go back to Zinc Binding Sites List in 2cex
Zinc binding site 6 out of 6 in the Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Sialic Acid Binding Protein (Siap) in the Presence of the Sialic Acid Acid Analogue NEU5AC2EN within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1307

b:21.1
occ:0.50
OD2 D:ASP4 1.7 34.6 1.0
OD2 D:ASP2 2.3 24.2 1.0
CG D:ASP4 2.4 35.5 1.0
OD1 D:ASP2 2.4 24.2 1.0
O D:HOH2122 2.5 21.4 1.0
OD1 D:ASP4 2.6 39.4 1.0
CG D:ASP2 2.7 32.2 1.0
CB D:ASP4 3.9 33.1 1.0
O D:HOH2001 4.0 29.8 1.0
CB D:ASP2 4.2 36.0 1.0
N D:ASP4 4.6 33.2 1.0
CA D:ASP4 4.8 33.0 1.0
C D:ASP2 4.9 36.0 1.0
CA D:ASP2 5.0 36.6 1.0

Reference:

A.Muller, E.Severi, C.Mulligan, A.G.Watts, D.J.Kelly, K.S.Wilson, A.J.Wilkinson, G.H.Thomas. Conservation of Structure and Mechanism in Primary and Secondary Transporters Exemplified By Siap, A Sialic Acid Binding Virulence Factor From Haemophilus Influenzae J.Biol.Chem. V. 281 22212 2006.
ISSN: ISSN 0021-9258
PubMed: 16702222
DOI: 10.1074/JBC.M603463200
Page generated: Wed Dec 16 03:19:12 2020

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