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Zinc in PDB 2ayi: Wild-Type Ampt From Thermus Thermophilus

Protein crystallography data

The structure of Wild-Type Ampt From Thermus Thermophilus, PDB code: 2ayi was solved by S.G.Odintsov, I.Sabala, G.Bourenkov, V.Rybin, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.70
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 246.472, 246.472, 51.135, 90.00, 90.00, 90.00
R / Rfree (%) 30.8 / 32.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Wild-Type Ampt From Thermus Thermophilus (pdb code 2ayi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Wild-Type Ampt From Thermus Thermophilus, PDB code: 2ayi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2ayi

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Zinc binding site 1 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:0.8
occ:1.00
OE1 A:GLU316 2.6 0.5 1.0
OD1 A:ASP378 2.7 0.5 1.0
NE2 A:HIS376 2.8 0.5 1.0
OD2 A:ASP378 2.9 0.5 1.0
CG A:ASP378 3.1 0.5 1.0
OE1 A:GLU340 3.2 0.7 1.0
ZN A:ZN501 3.3 0.8 1.0
OE2 A:GLU316 3.3 0.5 1.0
CD A:GLU316 3.3 0.5 1.0
CD2 A:HIS376 3.4 0.5 1.0
OE2 A:GLU340 3.4 0.7 1.0
CD A:GLU340 3.4 0.7 1.0
CE1 A:HIS376 4.0 0.5 1.0
OH A:TYR352 4.1 0.8 1.0
CE2 A:TYR352 4.2 0.8 1.0
CB A:ASP378 4.4 0.5 1.0
CG A:GLU340 4.5 0.7 1.0
CZ A:TYR352 4.5 0.8 1.0
CG A:HIS376 4.7 0.5 1.0
NE2 A:HIS345 4.7 0.7 1.0
CG A:GLU316 4.8 0.5 1.0
ND1 A:HIS376 5.0 0.5 1.0

Zinc binding site 2 out of 10 in 2ayi

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Zinc binding site 2 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:0.8
occ:1.00
OE1 A:GLU250 2.2 0.8 1.0
OE2 A:GLU316 2.2 0.5 1.0
NE2 A:HIS345 2.7 0.7 1.0
CD A:GLU250 2.9 0.8 1.0
OE2 A:GLU250 2.9 0.8 1.0
OE1 A:GLU340 3.0 0.7 1.0
ZN A:ZN500 3.3 0.8 1.0
CD A:GLU316 3.3 0.5 1.0
CE1 A:HIS345 3.5 0.7 1.0
OE1 A:GLU316 3.7 0.5 1.0
CD2 A:HIS345 3.8 0.7 1.0
CD A:GLU340 3.9 0.7 1.0
CG A:GLU250 4.4 0.8 1.0
CG A:GLU340 4.4 0.7 1.0
CD2 A:PHE252 4.5 0.5 1.0
CG A:GLU316 4.5 0.5 1.0
OD1 A:ASP378 4.7 0.5 1.0
ND1 A:HIS345 4.7 0.7 1.0
CB A:GLU340 4.7 0.7 1.0
CG A:PHE252 4.7 0.5 1.0
CB A:ALA318 4.8 0.5 1.0
CE2 A:PHE252 4.8 0.5 1.0
OE2 A:GLU340 4.8 0.7 1.0
CG A:HIS345 4.9 0.7 1.0

Zinc binding site 3 out of 10 in 2ayi

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Zinc binding site 3 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:0.8
occ:1.00
OE1 B:GLU316 2.5 0.5 1.0
OE1 B:GLU340 3.0 0.7 1.0
OD1 B:ASP378 3.1 0.5 1.0
OE2 B:GLU316 3.1 0.5 1.0
NE2 B:HIS376 3.1 0.5 1.0
CD B:GLU316 3.2 0.5 1.0
ZN B:ZN601 3.3 0.8 1.0
OD2 B:ASP378 3.3 0.5 1.0
CG B:ASP378 3.5 0.5 1.0
CD B:GLU340 3.5 0.7 1.0
OE2 B:GLU340 3.6 0.7 1.0
CD2 B:HIS376 3.8 0.5 1.0
CE2 B:TYR352 4.0 0.8 1.0
OH B:TYR352 4.2 0.8 1.0
CE1 B:HIS376 4.2 0.5 1.0
CZ B:TYR352 4.5 0.8 1.0
NE2 B:HIS345 4.6 0.7 1.0
CG B:GLU340 4.6 0.7 1.0
CG B:GLU316 4.6 0.5 1.0
CB B:ASP378 4.8 0.5 1.0
CD2 B:TYR352 5.0 0.8 1.0

Zinc binding site 4 out of 10 in 2ayi

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Zinc binding site 4 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:0.8
occ:1.00
NE2 B:HIS345 1.9 0.7 1.0
OE2 B:GLU316 2.0 0.5 1.0
OE1 B:GLU250 2.2 0.8 1.0
CE1 B:HIS345 2.7 0.7 1.0
CD2 B:HIS345 3.0 0.7 1.0
CD B:GLU250 3.1 0.8 1.0
CD B:GLU316 3.2 0.5 1.0
ZN B:ZN600 3.3 0.8 1.0
OE1 B:GLU340 3.3 0.7 1.0
OE2 B:GLU250 3.4 0.8 1.0
OE1 B:GLU316 3.8 0.5 1.0
ND1 B:HIS345 3.9 0.7 1.0
CD B:GLU340 4.0 0.7 1.0
CG B:HIS345 4.1 0.7 1.0
CB B:ALA318 4.2 0.5 1.0
CG B:GLU340 4.3 0.7 1.0
CG B:GLU316 4.4 0.5 1.0
OD1 B:ASP378 4.4 0.5 1.0
CG B:GLU250 4.5 0.8 1.0
CB B:GLU340 4.6 0.7 1.0
CD2 B:PHE252 4.8 0.5 1.0
CG B:ASP378 4.8 0.5 1.0
CG B:PHE252 4.9 0.5 1.0
O B:GLU340 4.9 0.7 1.0
OE2 B:GLU340 5.0 0.7 1.0

Zinc binding site 5 out of 10 in 2ayi

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Zinc binding site 5 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn700

b:0.8
occ:1.00
OE1 C:GLU316 2.2 0.5 1.0
NE2 C:HIS376 2.5 0.5 1.0
OD1 C:ASP378 2.9 0.5 1.0
CD C:GLU316 3.1 0.5 1.0
CD2 C:HIS376 3.2 0.5 1.0
ZN C:ZN701 3.2 0.8 1.0
OE2 C:GLU316 3.2 0.5 1.0
OD2 C:ASP378 3.3 0.5 1.0
CG C:ASP378 3.4 0.5 1.0
OE1 C:GLU340 3.6 0.7 1.0
CE1 C:HIS376 3.6 0.5 1.0
CE2 C:TYR352 3.8 0.8 1.0
OE2 C:GLU340 3.9 0.7 1.0
OH C:TYR352 3.9 0.8 1.0
CD C:GLU340 3.9 0.7 1.0
CZ C:TYR352 4.2 0.8 1.0
CG C:HIS376 4.5 0.5 1.0
CG C:GLU316 4.5 0.5 1.0
ND1 C:HIS376 4.6 0.5 1.0
CD2 C:TYR352 4.8 0.8 1.0
CB C:ASP378 4.8 0.5 1.0
NE2 C:HIS345 5.0 0.7 1.0

Zinc binding site 6 out of 10 in 2ayi

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Zinc binding site 6 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:0.8
occ:1.00
OE2 C:GLU316 2.1 0.5 1.0
OE1 C:GLU250 2.4 0.8 1.0
NE2 C:HIS345 2.5 0.7 1.0
OE1 C:GLU340 2.8 0.7 1.0
CD C:GLU250 3.1 0.8 1.0
OE2 C:GLU250 3.1 0.8 1.0
CD C:GLU316 3.2 0.5 1.0
ZN C:ZN700 3.2 0.8 1.0
CE1 C:HIS345 3.4 0.7 1.0
OE1 C:GLU316 3.6 0.5 1.0
CD2 C:HIS345 3.6 0.7 1.0
CD C:GLU340 3.7 0.7 1.0
CG C:GLU340 4.2 0.7 1.0
OD1 C:ASP378 4.4 0.5 1.0
CG C:GLU316 4.5 0.5 1.0
ND1 C:HIS345 4.6 0.7 1.0
CB C:GLU340 4.6 0.7 1.0
OE2 C:GLU340 4.6 0.7 1.0
CG C:GLU250 4.6 0.8 1.0
CG C:HIS345 4.7 0.7 1.0
CD2 C:PHE252 4.7 0.5 1.0
CG C:ASP378 4.8 0.5 1.0
CB C:ALA318 4.8 0.5 1.0
CG C:PHE252 4.9 0.5 1.0

Zinc binding site 7 out of 10 in 2ayi

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Zinc binding site 7 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn800

b:0.8
occ:1.00
OD1 D:ASP378 2.8 0.5 1.0
OE1 D:GLU340 2.8 0.7 1.0
ZN D:ZN801 2.8 0.8 1.0
OE1 D:GLU316 2.8 0.5 1.0
OD2 D:ASP378 2.9 0.5 1.0
CG D:ASP378 3.1 0.5 1.0
CD D:GLU340 3.1 0.7 1.0
OE2 D:GLU340 3.2 0.7 1.0
OE2 D:GLU316 3.2 0.5 1.0
NE2 D:HIS376 3.3 0.5 1.0
CD D:GLU316 3.4 0.5 1.0
CD2 D:HIS376 3.9 0.5 1.0
CG D:GLU340 4.1 0.7 1.0
CB D:ASP378 4.3 0.5 1.0
NE2 D:HIS345 4.4 0.7 1.0
CE1 D:HIS376 4.4 0.5 1.0
OH D:TYR352 4.5 0.8 1.0
CE2 D:TYR352 4.5 0.8 1.0
CD2 D:HIS345 4.8 0.7 1.0
CG D:GLU316 4.9 0.5 1.0
CZ D:TYR352 4.9 0.8 1.0

Zinc binding site 8 out of 10 in 2ayi

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Zinc binding site 8 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:0.8
occ:1.00
OE2 D:GLU316 2.1 0.5 1.0
OE1 D:GLU250 2.3 0.8 1.0
NE2 D:HIS345 2.7 0.7 1.0
ZN D:ZN800 2.8 0.8 1.0
OE1 D:GLU340 3.0 0.7 1.0
CD D:GLU250 3.0 0.8 1.0
OE2 D:GLU250 3.0 0.8 1.0
CD D:GLU316 3.1 0.5 1.0
OE1 D:GLU316 3.5 0.5 1.0
CE1 D:HIS345 3.5 0.7 1.0
CD2 D:HIS345 3.8 0.7 1.0
CD D:GLU340 3.9 0.7 1.0
CG D:GLU316 4.4 0.5 1.0
CG D:GLU340 4.4 0.7 1.0
CD2 D:PHE252 4.5 0.5 1.0
CG D:GLU250 4.5 0.8 1.0
OD1 D:ASP378 4.5 0.5 1.0
CG D:PHE252 4.7 0.5 1.0
CE2 D:PHE252 4.7 0.5 1.0
ND1 D:HIS345 4.7 0.7 1.0
CB D:ALA318 4.8 0.5 1.0
OE2 D:GLU340 4.8 0.7 1.0
CB D:GLU340 4.8 0.7 1.0
CG D:HIS345 4.9 0.7 1.0
CG D:ASP378 5.0 0.5 1.0

Zinc binding site 9 out of 10 in 2ayi

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Zinc binding site 9 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn900

b:0.8
occ:1.00
OE1 E:GLU316 2.7 0.5 1.0
OE1 E:GLU340 2.8 0.7 1.0
OE2 E:GLU316 3.1 0.5 1.0
OD1 E:ASP378 3.1 0.5 1.0
ZN E:ZN901 3.2 0.8 1.0
CD E:GLU340 3.2 0.7 1.0
CD E:GLU316 3.3 0.5 1.0
OD2 E:ASP378 3.3 0.5 1.0
NE2 E:HIS376 3.3 0.5 1.0
OE2 E:GLU340 3.4 0.7 1.0
CG E:ASP378 3.4 0.5 1.0
CD2 E:HIS376 4.0 0.5 1.0
CE2 E:TYR352 4.2 0.8 1.0
CG E:GLU340 4.4 0.7 1.0
OH E:TYR352 4.4 0.8 1.0
NE2 E:HIS345 4.4 0.7 1.0
CE1 E:HIS376 4.5 0.5 1.0
CZ E:TYR352 4.7 0.8 1.0
CB E:ASP378 4.7 0.5 1.0
CG E:GLU316 4.8 0.5 1.0
CD2 E:HIS345 4.9 0.7 1.0
OE1 E:GLU250 4.9 0.8 1.0

Zinc binding site 10 out of 10 in 2ayi

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Zinc binding site 10 out of 10 in the Wild-Type Ampt From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Wild-Type Ampt From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn901

b:0.8
occ:1.00
OE1 E:GLU250 1.9 0.8 1.0
OE2 E:GLU316 2.0 0.5 1.0
NE2 E:HIS345 2.2 0.7 1.0
CD E:GLU250 2.9 0.8 1.0
CE1 E:HIS345 3.0 0.7 1.0
CD E:GLU316 3.1 0.5 1.0
OE2 E:GLU250 3.2 0.8 1.0
ZN E:ZN900 3.2 0.8 1.0
CD2 E:HIS345 3.4 0.7 1.0
OE1 E:GLU340 3.5 0.7 1.0
OE1 E:GLU316 3.8 0.5 1.0
CB E:ALA318 4.1 0.5 1.0
ND1 E:HIS345 4.2 0.7 1.0
CG E:GLU316 4.3 0.5 1.0
CG E:GLU250 4.3 0.8 1.0
CD E:GLU340 4.3 0.7 1.0
CD2 E:PHE252 4.3 0.5 1.0
CG E:HIS345 4.4 0.7 1.0
CG E:PHE252 4.5 0.5 1.0
CG E:GLU340 4.6 0.7 1.0
OD1 E:ASP378 4.7 0.5 1.0
CB E:PHE252 4.7 0.5 1.0
CE2 E:PHE252 4.8 0.5 1.0
CB E:GLU250 4.9 0.8 1.0
CB E:GLU340 4.9 0.7 1.0

Reference:

S.G.Odintsov, I.Sabala, G.Bourenkov, V.Rybin, M.Bochtler. Substrate Access to the Active Sites in Aminopeptidase T, A Representative of A New Metallopeptidase Clan. J.Mol.Biol. V. 354 403 2005.
ISSN: ISSN 0022-2836
PubMed: 16242715
DOI: 10.1016/J.JMB.2005.09.042
Page generated: Wed Dec 16 03:17:57 2020

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