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Zinc in PDB 4kay: Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn

Enzymatic activity of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn

All present enzymatic activity of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn:
3.1.3.27;

Protein crystallography data

The structure of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn, PDB code: 4kay was solved by A.Vrielink, C.Wanty, A.Anandan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.068, 90.517, 91.176, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 19

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn (pdb code 4kay). 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 the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn, PDB code: 4kay:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4kay

Go back to Zinc Binding Sites List in 4kay
Zinc binding site 1 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:11.1
occ:1.00
 OE2 A:GLU240 1.8 6.6 1.0
OD2 A:ASP452 2.0 12.1 1.0
OG1 A:TPO280 2.0 11.3 1.0
NE2 A:HIS453 2.0 10.0 1.0
CD A:GLU240 2.4 13.9 1.0
OE1 A:GLU240 2.4 13.0 1.0
CG A:ASP452 2.9 13.7 1.0
O2P A:TPO280 2.9 32.7 1.0
CD2 A:HIS453 2.9 9.3 1.0
CE1 A:HIS453 3.0 7.5 1.0
HD2 A:HIS453 3.0 11.1 1.0
P A:TPO280 3.0 48.7 1.0
OD1 A:ASP452 3.1 9.4 1.0
CB A:TPO280 3.2 13.8 1.0
HG22 A:TPO280 3.2 16.8 1.0
HE1 A:HIS453 3.2 9.0 1.0
HA A:TPO280 3.4 12.3 1.0
H A:TPO280 3.4 14.6 1.0
CA A:TPO280 3.6 10.2 1.0
CG2 A:TPO280 3.6 14.0 1.0
N A:TPO280 3.6 12.2 1.0
O3P A:TPO280 3.8 24.4 1.0
HG21 A:TPO280 3.9 16.8 1.0
HD2 A:HIS383 3.9 30.3 1.0
CG A:GLU240 3.9 7.2 1.0
CG A:HIS453 4.0 8.7 1.0
ND1 A:HIS453 4.0 9.5 1.0
HA A:GLU240 4.0 9.5 1.0
HG1 A:THR241 4.0 13.0 1.0
HB A:TPO280 4.0 16.5 1.0
H A:THR241 4.1 10.9 1.0
O A:HOH712 4.2 8.4 1.0
HG3 A:GLU240 4.2 8.6 1.0
CB A:ASP452 4.2 8.8 1.0
HB2 A:ASP452 4.3 10.5 1.0
O1P A:TPO280 4.3 47.1 1.0
OG1 A:THR241 4.3 10.8 1.0
ZN A:ZN602 4.3 21.6 0.7
HA A:SER279 4.4 14.6 1.0
HG2 A:GLU240 4.4 8.6 1.0
NE2 A:HIS465 4.5 16.2 1.0
C A:SER279 4.5 13.3 1.0
N A:THR241 4.5 9.1 1.0
HB3 A:ASP452 4.6 10.5 1.0
HG23 A:TPO280 4.6 16.8 1.0
CD2 A:HIS383 4.6 25.3 1.0
CA A:GLU240 4.7 7.9 1.0
CB A:GLU240 4.7 7.9 1.0
HB2 A:GLU240 4.7 9.5 1.0
HD1 A:HIS453 4.7 11.4 1.0
CE1 A:HIS465 4.9 17.9 1.0
HA A:THR241 4.9 9.3 1.0
OD2 A:ASP324 5.0 12.3 1.0
NE2 A:HIS383 5.0 20.2 1.0
CD2 A:HIS465 5.0 10.9 1.0
C A:GLU240 5.0 11.5 1.0

Zinc binding site 2 out of 6 in 4kay

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Zinc binding site 2 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:21.6
occ:0.70
 O2P A:TPO280 2.0 32.7 1.0
NE2 A:HIS383 2.2 20.2 1.0
NE2 A:HIS465 2.3 16.2 1.0
O3P A:TPO280 2.5 24.4 1.0
HE1 A:HIS465 2.6 21.5 1.0
P A:TPO280 2.7 48.7 1.0
CE1 A:HIS465 2.8 17.9 1.0
CE1 A:HIS383 3.0 23.6 1.0
HE1 A:HIS383 3.1 28.3 1.0
CD2 A:HIS383 3.2 25.3 1.0
O1P A:TPO280 3.4 47.1 1.0
HD2 A:HIS383 3.5 30.3 1.0
CD2 A:HIS465 3.6 10.9 1.0
OG1 A:TPO280 4.0 11.3 1.0
HD2 A:HIS465 4.0 13.1 1.0
ND1 A:HIS465 4.1 13.8 1.0
ND1 A:HIS383 4.2 21.2 1.0
HE1 A:HIS453 4.2 9.0 1.0
CG A:HIS383 4.3 15.1 1.0
ZN A:ZN601 4.3 11.1 1.0
N B:ASN211 4.4 34.3 0.8
H A:TPO280 4.5 14.6 1.0
CG A:HIS465 4.5 11.9 1.0
OE2 A:GLU240 4.5 6.6 1.0
NE2 A:HIS453 4.6 10.0 1.0
HG1 A:THR241 4.7 13.0 1.0
OD1 B:ASN211 4.7 17.9 0.8
CE1 A:HIS453 4.7 7.5 1.0
HD1 A:HIS465 4.7 16.6 1.0
HA B:ASN211 4.8 38.9 0.8
HD1 A:HIS383 4.9 25.4 1.0
O A:HOH817 5.0 16.8 1.0

Zinc binding site 3 out of 6 in 4kay

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Zinc binding site 3 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:51.4
occ:1.00
 NE2 A:HIS303 2.2 19.8 1.0
CE1 A:HIS303 3.0 18.8 1.0
HE1 A:HIS303 3.0 22.6 1.0
HG23 A:ILE212 3.2 51.2 1.0
CD2 A:HIS303 3.3 27.9 1.0
H A:ILE212 3.5 44.1 0.8
HD2 A:HIS303 3.5 33.5 1.0
N A:ASN211 3.9 26.9 0.8
CG2 A:ILE212 4.1 42.7 1.0
ND1 A:HIS303 4.2 15.4 1.0
HG22 A:ILE212 4.3 51.2 1.0
CG A:HIS303 4.3 17.9 1.0
N A:ILE212 4.4 36.8 1.0
O A:ILE212 4.4 28.1 1.0
HG21 A:ILE212 4.5 51.2 1.0
O A:HOH985 4.6 28.9 1.0
HD13 A:ILE212 4.8 39.9 1.0
HG12 A:ILE212 4.9 46.6 1.0
HD1 A:HIS303 4.9 18.4 1.0

Zinc binding site 4 out of 6 in 4kay

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Zinc binding site 4 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:10.8
occ:1.00
 OE2 B:GLU240 1.8 5.8 1.0
OG1 B:TPO280 2.0 10.3 1.0
OD2 B:ASP452 2.0 12.8 1.0
NE2 B:HIS453 2.0 9.2 1.0
OE1 B:GLU240 2.3 11.0 1.0
CD B:GLU240 2.3 11.7 1.0
O2P B:TPO280 2.8 34.3 1.0
CG B:ASP452 2.9 11.2 1.0
CD2 B:HIS453 2.9 8.5 1.0
CE1 B:HIS453 3.0 8.9 1.0
P B:TPO280 3.0 54.3 1.0
HD2 B:HIS453 3.1 10.2 1.0
OD1 B:ASP452 3.1 8.8 1.0
CB B:TPO280 3.2 11.9 1.0
HG22 B:TPO280 3.2 14.2 1.0
HE1 B:HIS453 3.2 10.7 1.0
H B:TPO280 3.3 14.9 1.0
HA B:TPO280 3.3 10.9 1.0
CA B:TPO280 3.6 9.1 1.0
N B:TPO280 3.6 12.4 1.0
CG2 B:TPO280 3.6 11.9 1.0
O3P B:TPO280 3.8 25.0 1.0
CG B:GLU240 3.8 8.7 1.0
HG21 B:TPO280 3.9 14.2 1.0
HD2 B:HIS383 3.9 25.5 1.0
ND1 B:HIS453 4.0 9.4 1.0
CG B:HIS453 4.0 9.8 1.0
HG1 B:THR241 4.0 13.4 1.0
HA B:GLU240 4.0 10.5 1.0
HB B:TPO280 4.0 14.2 1.0
H B:THR241 4.1 10.1 1.0
HG3 B:GLU240 4.1 10.4 1.0
HE2 B:HIS465 4.2 19.9 1.0
O1P B:TPO280 4.2 50.3 1.0
CB B:ASP452 4.2 9.5 1.0
OG1 B:THR241 4.2 11.2 1.0
O B:HOH725 4.2 10.8 1.0
HG2 B:GLU240 4.3 10.4 1.0
HB2 B:ASP452 4.3 11.4 1.0
ZN B:ZN602 4.4 23.7 0.7
HA B:SER279 4.4 18.7 1.0
C B:SER279 4.5 17.0 1.0
NE2 B:HIS465 4.5 16.6 1.0
N B:THR241 4.5 8.4 1.0
HG23 B:TPO280 4.6 14.2 1.0
HB3 B:ASP452 4.6 11.4 1.0
CB B:GLU240 4.6 8.5 1.0
HB2 B:GLU240 4.6 10.2 1.0
CD2 B:HIS383 4.7 21.2 1.0
CA B:GLU240 4.7 8.7 1.0
HD1 B:HIS453 4.7 11.3 1.0
CE1 B:HIS465 4.9 14.0 1.0
NE2 B:HIS383 5.0 18.9 1.0
HA B:THR241 5.0 8.6 1.0
CD2 B:HIS465 5.0 12.2 1.0
C B:GLU240 5.0 9.7 1.0

Zinc binding site 5 out of 6 in 4kay

Go back to Zinc Binding Sites List in 4kay
Zinc binding site 5 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:23.7
occ:0.68
 HE2 B:HIS465 1.7 19.9 1.0
O2P B:TPO280 2.0 34.3 1.0
NE2 B:HIS383 2.2 18.9 1.0
NE2 B:HIS465 2.5 16.6 1.0
O3P B:TPO280 2.5 25.0 1.0
P B:TPO280 2.6 54.3 1.0
HE1 B:HIS465 2.8 16.8 1.0
CE1 B:HIS465 3.0 14.0 1.0
CE1 B:HIS383 3.0 22.7 1.0
HE1 B:HIS383 3.1 27.2 1.0
O1P B:TPO280 3.2 50.3 1.0
CD2 B:HIS383 3.3 21.2 1.0
HD2 B:HIS383 3.5 25.5 1.0
CD2 B:HIS465 3.7 12.2 1.0
OG1 B:TPO280 4.0 10.3 1.0
O A:HOH1255 4.1 21.8 1.0
HD2 B:HIS465 4.1 14.7 1.0
ND1 B:HIS383 4.2 18.3 1.0
ND1 B:HIS465 4.2 12.5 1.0
CG B:HIS383 4.3 12.2 1.0
ZN B:ZN601 4.4 10.8 1.0
HE1 B:HIS453 4.4 10.7 1.0
N A:ASN211 4.4 26.9 0.8
H B:TPO280 4.5 14.9 1.0
OE2 B:GLU240 4.5 5.8 1.0
CG B:HIS465 4.6 10.3 1.0
NE2 B:HIS453 4.7 9.2 1.0
OD1 A:ASN211 4.8 18.0 0.8
HA A:ASN211 4.8 36.8 0.8
HG1 B:THR241 4.8 13.4 1.0
CE1 B:HIS453 4.8 8.9 1.0
HD1 B:HIS465 4.9 15.0 1.0
HD1 B:HIS383 4.9 21.9 1.0
O B:HOH800 5.0 17.6 1.0

Zinc binding site 6 out of 6 in 4kay

Go back to Zinc Binding Sites List in 4kay
Zinc binding site 6 out of 6 in the Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis - Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:51.6
occ:1.00
 NE2 B:HIS303 2.2 19.1 1.0
CE1 B:HIS303 3.0 19.2 1.0
HE1 B:HIS303 3.0 23.1 1.0
HG23 B:ILE212 3.2 51.0 1.0
CD2 B:HIS303 3.3 30.5 1.0
H B:ILE212 3.5 44.3 0.8
HD2 B:HIS303 3.6 36.6 1.0
N B:ASN211 3.9 34.3 0.8
CG2 B:ILE212 4.1 42.5 1.0
ND1 B:HIS303 4.2 13.3 1.0
HG22 B:ILE212 4.3 51.0 1.0
CG B:HIS303 4.4 18.1 1.0
N B:ILE212 4.4 37.0 1.0
HG21 B:ILE212 4.5 51.0 1.0
O B:ILE212 4.5 30.9 1.0
HD13 B:ILE212 4.7 37.1 1.0
O B:HOH976 4.8 26.9 1.0
HG12 B:ILE212 4.9 46.4 1.0
HD1 B:HIS303 4.9 16.0 1.0

Reference:

C.Wanty, A.Anandan, S.Piek, J.Walshe, J.Ganguly, R.W.Carlson, K.A.Stubbs, C.M.Kahler, A.Vrielink. The Structure of the Neisserial Lipooligosaccharide Phosphoethanolamine Transferase A (Lpta) Required For Resistance to Polymyxin. J.Mol.Biol. V. 425 3389 2013.
ISSN: ISSN 0022-2836
PubMed: 23810904
DOI: 10.1016/J.JMB.2013.06.029
Page generated: Sun Oct 27 01:05:54 2024

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