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Zinc in PDB 1waa: IG27 Protein Domain

Protein crystallography data

The structure of IG27 Protein Domain, PDB code: 1waa was solved by M.C.Vega, L.Valencia, P.Zou, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.240, 75.990, 134.220, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the IG27 Protein Domain (pdb code 1waa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the IG27 Protein Domain, PDB code: 1waa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 1waa

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Zinc binding site 1 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1090

b:37.3
occ:1.00
ND1 E:HIS20 1.9 35.4 1.0
ND1 A:HIS20 2.0 39.4 1.0
O A:HOH2098 2.4 14.7 1.0
O A:HOH2099 2.7 11.8 1.0
CE1 E:HIS20 2.7 37.7 1.0
CE1 A:HIS20 2.7 34.9 1.0
CG A:HIS20 2.9 32.9 1.0
CG E:HIS20 2.9 32.7 1.0
CB A:HIS20 3.4 31.0 1.0
CB E:HIS20 3.4 29.1 1.0
NE2 A:HIS20 3.8 41.6 1.0
CD2 A:HIS20 3.9 35.5 1.0
NE2 E:HIS20 3.9 35.4 1.0
CD2 E:HIS20 4.0 36.0 1.0
N A:HIS20 4.0 30.2 1.0
N E:HIS20 4.1 27.0 1.0
CA A:HIS20 4.3 30.2 1.0
CA E:HIS20 4.4 28.1 1.0
O E:HOH2010 4.6 31.7 1.0
O A:THR18 4.7 27.0 1.0
O E:THR18 4.8 27.9 1.0
C A:ALA19 4.8 29.1 1.0
O A:HIS20 4.9 28.6 1.0
O E:HIS20 4.9 30.2 1.0
C E:ALA19 4.9 25.7 1.0

Zinc binding site 2 out of 24 in 1waa

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Zinc binding site 2 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1091

b:24.7
occ:1.00
OE1 E:GLU22 1.8 39.8 1.0
OE1 A:GLU48 1.9 27.4 1.0
NE2 A:HIS61 2.1 27.1 1.0
O A:HOH2100 2.2 21.0 1.0
CD E:GLU22 2.5 32.7 1.0
OE2 E:GLU22 2.6 36.5 1.0
CD A:GLU48 2.9 29.8 1.0
CD2 A:HIS61 3.1 26.7 1.0
CE1 A:HIS61 3.1 27.3 1.0
OE2 A:GLU48 3.2 35.0 1.0
O E:HOH2008 3.7 29.7 1.0
NZ E:LYS55 3.8 32.6 1.0
CG E:GLU22 3.8 33.6 1.0
CG2 A:ILE59 4.2 27.0 1.0
ND1 A:HIS61 4.2 25.9 1.0
CG A:HIS61 4.2 23.9 1.0
CG A:GLU48 4.3 26.4 1.0
CE E:LYS55 4.4 38.4 1.0
CD1 A:ILE59 4.6 27.5 1.0
O A:PRO45 4.7 32.1 1.0
O E:HOH2020 4.9 42.1 1.0
CB A:ILE59 4.9 26.4 1.0
CB A:GLU48 4.9 24.9 1.0
CB E:GLU22 4.9 29.2 1.0

Zinc binding site 3 out of 24 in 1waa

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Zinc binding site 3 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1092

b:31.6
occ:1.00
OD1 B:ASP29 2.0 30.0 1.0
OD2 F:ASP29 2.0 33.6 1.0
O A:HOH2101 2.1 22.2 1.0
OD1 A:ASP29 2.1 31.3 1.0
OD2 A:ASP29 2.7 35.5 1.0
OD1 F:ASP29 2.7 26.8 1.0
CG F:ASP29 2.7 25.2 1.0
CG A:ASP29 2.7 30.8 1.0
CG B:ASP29 2.8 26.2 1.0
OD2 B:ASP29 2.8 28.6 1.0
O F:HOH2034 3.3 40.9 1.0
CB F:ASP29 4.2 25.2 1.0
CB B:ASP29 4.2 24.5 1.0
CB A:ASP29 4.2 25.4 1.0
O A:HOH2065 4.2 27.2 1.0
CB F:PRO28 4.8 22.8 1.0
CB A:PRO28 4.8 23.2 1.0
O B:HOH2032 4.8 31.3 1.0
CB B:PRO28 5.0 25.1 1.0

Zinc binding site 4 out of 24 in 1waa

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Zinc binding site 4 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1093

b:33.5
occ:0.80
O A:HOH2103 1.9 33.0 1.0
OD1 B:ASP52 1.9 28.8 1.0
NE2 A:HIS31 2.0 42.0 1.0
O A:HOH2102 2.4 36.5 1.0
OD2 B:ASP52 2.6 24.7 1.0
CG B:ASP52 2.6 25.7 1.0
CE1 A:HIS31 2.9 41.7 1.0
CD2 A:HIS31 3.0 34.6 1.0
O A:HOH2039 3.3 15.2 1.0
ND1 A:HIS31 4.0 37.6 1.0
CB B:ASP52 4.1 23.0 1.0
CG A:HIS31 4.1 32.8 1.0
O A:ASP29 4.5 25.0 1.0
C B:ASP52 4.6 24.4 1.0
CA B:ASP52 4.7 23.5 1.0
O B:HOH2050 4.7 34.2 1.0
N B:GLY53 4.7 24.7 1.0
O D:GLU51 4.8 25.1 1.0
N D:GLU51 4.9 24.4 1.0
O B:ASP52 4.9 24.1 1.0

Zinc binding site 5 out of 24 in 1waa

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Zinc binding site 5 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1094

b:43.4
occ:0.80
O A:HOH2105 2.2 39.6 1.0
OE1 A:GLU88 2.5 42.5 1.0
O A:HOH2104 2.8 45.0 1.0
CD A:GLU88 3.5 36.8 1.0
OE2 A:GLU88 3.9 39.3 1.0
CG A:GLU88 4.7 36.6 1.0

Zinc binding site 6 out of 24 in 1waa

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Zinc binding site 6 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1090

b:25.6
occ:1.00
OE1 B:GLU48 1.8 33.7 1.0
OE1 D:GLU22 2.0 30.5 1.0
O B:HOH2079 2.0 17.6 1.0
NE2 B:HIS61 2.0 26.4 1.0
CD B:GLU48 2.7 31.8 1.0
CD D:GLU22 2.9 31.1 1.0
CD2 B:HIS61 3.0 25.8 1.0
OE2 B:GLU48 3.0 37.2 1.0
OE2 D:GLU22 3.0 30.8 1.0
CE1 B:HIS61 3.1 27.1 1.0
NZ D:LYS55 3.7 39.1 1.0
O D:HOH2023 3.8 33.0 1.0
O D:HOH2024 3.8 27.0 1.0
O B:HOH2046 3.9 27.3 1.0
CG2 B:ILE59 4.1 28.4 1.0
CG B:GLU48 4.1 27.7 1.0
CG B:HIS61 4.1 26.9 1.0
ND1 B:HIS61 4.2 30.6 1.0
CG D:GLU22 4.3 29.0 1.0
CE D:LYS55 4.4 44.7 1.0
O B:PRO45 4.7 32.1 1.0
CD1 B:ILE59 4.8 26.9 1.0
CB B:GLU48 4.8 26.1 1.0
CB B:ILE59 5.0 26.4 1.0

Zinc binding site 7 out of 24 in 1waa

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Zinc binding site 7 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1091

b:25.9
occ:0.80
ND1 B:HIS31 2.0 31.4 1.0
O B:HOH2082 2.1 26.5 1.0
O B:HOH2080 2.1 19.9 1.0
O B:HOH2081 2.1 20.2 1.0
OE2 C:GLU51 2.2 25.1 1.0
OE1 C:GLU51 2.5 32.2 1.0
CD C:GLU51 2.7 29.9 1.0
CE1 B:HIS31 2.9 31.1 1.0
CG B:HIS31 3.1 29.9 1.0
CB B:HIS31 3.6 25.0 1.0
O C:HOH2047 4.0 31.8 1.0
O B:HOH2030 4.0 33.2 1.0
NE2 B:HIS31 4.1 28.9 1.0
OE2 B:GLU51 4.1 25.9 0.5
OE1 B:GLU51 4.1 20.7 0.5
O C:ILE49 4.1 26.6 1.0
CA B:HIS31 4.1 26.8 1.0
CG C:GLU51 4.2 26.4 1.0
CD2 B:HIS31 4.2 31.9 1.0
OD2 F:ASP52 4.3 32.8 1.0
CD B:GLU51 4.5 29.4 0.5
O C:HOH2046 4.8 23.3 1.0
N C:GLU51 4.9 23.7 1.0
CB C:GLU51 4.9 26.0 1.0
C C:ILE49 4.9 27.6 1.0
OD1 F:ASP52 5.0 37.4 1.0

Zinc binding site 8 out of 24 in 1waa

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Zinc binding site 8 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1092

b:36.5
occ:0.80
OE2 B:GLU3 2.0 39.4 1.0
O B:HOH2083 2.3 36.8 1.0
CD B:GLU3 2.8 37.1 1.0
OE1 B:GLU3 2.9 40.2 1.0
CG B:GLU3 4.2 31.7 1.0
O B:HOH2087 4.4 33.0 1.0
CD1 B:LEU1 4.4 20.0 0.0

Zinc binding site 9 out of 24 in 1waa

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Zinc binding site 9 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1093

b:24.4
occ:0.50
O B:HOH2084 1.9 26.1 1.0
ND1 B:HIS20 2.0 45.9 1.0
O B:HOH2085 2.0 17.6 1.0
ND1 D:HIS20 2.0 41.7 1.0
CG B:HIS20 2.8 38.5 1.0
CG D:HIS20 2.9 37.5 1.0
CE1 D:HIS20 3.0 34.6 1.0
CE1 B:HIS20 3.1 43.0 1.0
CB B:HIS20 3.1 32.1 1.0
CB D:HIS20 3.2 33.7 1.0
O D:HOH2020 3.5 21.1 1.0
O B:HOH2017 3.7 21.2 1.0
CD2 B:HIS20 4.0 46.7 1.0
NE2 D:HIS20 4.1 41.1 1.0
CD2 D:HIS20 4.1 42.1 1.0
NE2 B:HIS20 4.1 45.2 1.0
N D:HIS20 4.1 29.3 1.0
N B:HIS20 4.2 29.6 1.0
CA B:HIS20 4.2 29.7 1.0
CA D:HIS20 4.3 30.0 1.0
O D:HOH2012 4.8 34.9 1.0
C D:ALA19 4.9 28.9 1.0
C B:ALA19 4.9 27.7 1.0

Zinc binding site 10 out of 24 in 1waa

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Zinc binding site 10 out of 24 in the IG27 Protein Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of IG27 Protein Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1094

b:26.8
occ:0.50
O B:HOH2088 2.1 28.1 1.0
OE1 B:GLU5 2.3 31.4 1.0
O B:HOH2087 2.4 33.0 1.0
O B:HOH2086 2.4 21.5 1.0
OE2 B:GLU5 2.7 39.6 1.0
CD B:GLU5 2.8 37.0 1.0
N A:ALA-2 3.4 34.8 1.0
OE1 B:GLU3 3.7 40.2 1.0
CG B:GLU5 4.4 28.2 1.0
O B:HOH2083 4.4 36.8 1.0
O B:VAL4 4.5 23.7 1.0
CG A:MET-1 4.7 39.4 1.0
CA B:GLU5 4.7 25.7 1.0
CA A:ALA-2 4.8 34.4 1.0
CB B:GLU5 5.0 26.5 1.0
C A:ALA-2 5.0 33.6 1.0

Reference:

W.Stacklies, M.C.Vega, M.Wilmanns, F.Grater. Mechanical Network in Titin Immunoglobulin From Force Distribution Analysis. Plos Comput.Biol. V. 5 00306 2009.
ISSN: ISSN 1553-734X
PubMed: 19282960
DOI: 10.1371/JOURNAL.PCBI.1000306
Page generated: Mon Jan 25 16:15:25 2021

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