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Calcium in PDB 1yn8: SH3 Domain of Yeast NBP2

Protein crystallography data

The structure of SH3 Domain of Yeast NBP2, PDB code: 1yn8 was solved by P.Kursula, I.Kursula, Y.H.Song, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 32.410, 53.300, 57.830, 111.94, 90.98, 104.18
R / Rfree (%) 16.4 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the SH3 Domain of Yeast NBP2 (pdb code 1yn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the SH3 Domain of Yeast NBP2, PDB code: 1yn8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1yn8

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Calcium binding site 1 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:27.4
occ:1.00
 O E:HOH1051 2.3 29.7 1.0
O B:HOH1065 2.3 34.2 1.0
OE1 B:GLU53 2.3 26.0 1.0
O B:HOH1018 2.5 21.1 1.0
O B:HOH1052 2.5 33.4 1.0
O E:HOH1066 2.5 39.4 1.0
O E:HOH1096 2.6 41.4 1.0
CD B:GLU53 3.5 23.9 1.0
OE2 B:GLU53 3.9 23.4 1.0
NE1 E:TRP36 4.2 25.3 1.0
O B:HOH1037 4.4 37.7 1.0
CG B:GLU53 4.7 20.6 1.0
CD1 E:TRP36 4.8 25.8 1.0
O B:GLU53 4.8 23.9 1.0
O B:HOH1039 4.8 33.0 1.0
CB B:GLU53 4.8 21.9 1.0
CA B:GLU53 4.9 22.1 1.0

Calcium binding site 2 out of 10 in 1yn8

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Calcium binding site 2 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:29.5
occ:1.00
 O E:HOH1052 2.0 38.4 1.0
O B:HOH1077 2.3 39.0 1.0
OE1 E:GLU13 2.3 22.5 1.0
O B:HOH1026 2.3 35.2 1.0
O B:HOH1041 2.4 35.2 1.0
OE1 B:GLU22 2.5 28.9 1.0
O E:HOH1074 2.5 41.5 1.0
O E:HOH1031 2.7 31.2 1.0
OE2 B:GLU22 3.0 25.5 1.0
CD B:GLU22 3.1 28.1 1.0
CA E:CA1005 3.4 31.8 1.0
CD E:GLU13 3.4 23.0 1.0
O E:HOH1063 4.0 42.6 1.0
OE2 E:GLU13 4.0 30.0 1.0
O C:HOH1045 4.4 32.5 1.0
CG E:GLU13 4.4 24.8 1.0
CG B:GLU22 4.6 27.9 1.0
CB E:GLU13 4.6 25.5 1.0
O B:HOH1047 4.6 35.3 1.0
O E:HOH1062 4.6 31.8 1.0
OH C:TYR8 4.7 26.9 1.0
O B:HOH1020 4.9 28.2 1.0
O E:GLU13 5.0 26.1 1.0

Calcium binding site 3 out of 10 in 1yn8

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Calcium binding site 3 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1007

b:36.2
occ:1.00
 O B:HOH1050 2.2 30.0 1.0
OE1 B:GLU13 2.3 26.6 1.0
O B:HOH1087 2.4 34.3 1.0
O B:HOH1027 2.7 34.0 1.0
O E:HOH1094 3.2 43.4 1.0
CD B:GLU13 3.5 28.5 1.0
CA B:CA1008 4.0 46.3 1.0
CG B:GLU13 4.3 26.4 1.0
CB B:GLU13 4.3 24.5 1.0
OE2 B:GLU13 4.3 27.0 1.0
CD E:GLU22 4.4 37.2 1.0
OE2 E:GLU22 4.5 39.0 1.0
O E:HOH1019 4.5 24.6 1.0
OE1 E:GLU22 4.6 42.7 1.0
CG E:GLU22 4.7 27.8 1.0
O B:GLU13 4.7 25.5 1.0
O B:HOH1085 4.9 27.1 1.0

Calcium binding site 4 out of 10 in 1yn8

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Calcium binding site 4 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1008

b:46.3
occ:1.00
 O E:HOH1094 2.2 43.4 1.0
OE2 B:GLU13 2.4 27.0 1.0
O B:HOH1087 2.6 34.3 1.0
OE1 B:GLU13 2.7 26.6 1.0
CD B:GLU13 2.9 28.5 1.0
CA B:CA1007 4.0 36.2 1.0
O E:HOH1068 4.3 51.0 1.0
CG B:GLU13 4.4 26.4 1.0
CB E:GLU22 4.5 26.7 1.0
O B:HOH1010 4.6 19.4 1.0
OE1 E:GLU22 4.6 42.7 1.0
CG E:GLU22 4.7 27.8 1.0
CD E:GLU22 5.0 37.2 1.0

Calcium binding site 5 out of 10 in 1yn8

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Calcium binding site 5 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:19.9
occ:1.00
 O B:TYR57 2.3 21.1 1.0
O B:HOH1084 2.4 25.7 1.0
O C:HOH1068 2.4 34.1 1.0
O C:HOH1069 2.4 21.5 1.0
O B:HOH1083 2.4 28.4 1.0
OE2 C:GLU53 2.5 22.9 1.0
CD C:GLU53 3.4 22.7 1.0
C B:TYR57 3.6 22.8 1.0
OE1 C:GLU53 3.7 24.4 1.0
OG B:SER56 4.2 28.1 1.0
CA B:ILE58 4.3 25.2 1.0
N B:ILE58 4.4 23.1 1.0
N B:TYR57 4.6 25.0 1.0
OE2 C:GLU52 4.6 33.9 0.5
N B:GLN59 4.6 28.6 1.0
CA B:TYR57 4.6 24.4 1.0
OE2 C:GLU52 4.6 24.6 0.5
CA C:GLY35 4.6 27.7 1.0
O B:HOH1012 4.7 24.9 1.0
CG C:GLU53 4.8 22.8 1.0
O C:HOH1053 4.8 35.6 1.0
OXT B:GLN59 4.8 33.2 1.0
O C:GLY35 4.8 28.9 1.0
C B:SER56 5.0 25.4 1.0

Calcium binding site 6 out of 10 in 1yn8

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Calcium binding site 6 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1006

b:37.0
occ:1.00
 OE1 D:GLU13 2.3 33.5 1.0
O D:HOH1066 2.4 44.2 1.0
O D:HOH1051 2.6 37.5 1.0
CD D:GLU13 3.5 28.2 1.0
O D:HOH1064 3.6 48.7 1.0
CA D:CA1009 3.6 47.1 1.0
OE2 D:GLU13 4.3 32.2 1.0
CG D:GLU13 4.4 28.4 1.0
CB D:GLU13 4.4 25.5 1.0
O D:GLU13 4.8 24.2 1.0
CA D:GLU13 5.0 25.3 1.0
O D:HOH1081 5.0 37.1 1.0

Calcium binding site 7 out of 10 in 1yn8

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Calcium binding site 7 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1009

b:47.1
occ:1.00
 OE2 D:GLU13 2.4 32.2 1.0
O D:HOH1081 2.6 37.1 1.0
O D:HOH1066 2.6 44.2 1.0
OE1 D:GLU13 2.7 33.5 1.0
CD D:GLU13 2.9 28.2 1.0
CA D:CA1006 3.6 37.0 1.0
CG D:GLU13 4.4 28.4 1.0
O D:HOH1014 4.5 22.6 1.0
O D:HOH1051 4.6 37.5 1.0

Calcium binding site 8 out of 10 in 1yn8

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Calcium binding site 8 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1010

b:45.2
occ:1.00
 OE1 D:GLU22 2.4 31.4 0.5
CD D:GLU22 3.4 28.2 0.5
OE2 D:GLU22 4.0 29.5 0.5
OE1 D:GLU22 4.1 25.5 0.5
O D:HOH1055 4.5 34.2 1.0
CG D:GLU22 4.5 27.5 0.5
CB D:GLU22 4.5 26.4 0.5
O D:HOH1074 4.5 41.9 1.0
CB D:GLU22 4.6 25.0 0.5
CG D:GLU22 4.7 24.4 0.5
CD D:GLU22 4.8 22.7 0.5

Calcium binding site 9 out of 10 in 1yn8

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Calcium binding site 9 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1002

b:19.1
occ:1.00
 O E:HOH1089 2.3 17.7 1.0
O E:HOH1090 2.4 22.6 1.0
OD1 E:ASP24 2.4 25.1 1.0
O E:HOH1091 2.5 22.7 1.0
O E:HOH1087 2.5 18.0 1.0
O E:HOH1088 2.6 17.3 1.0
O E:HOH1086 2.6 23.9 1.0
O E:HOH1092 2.6 19.8 1.0
CG E:ASP24 3.6 28.1 1.0
OD2 E:ASP24 4.2 26.0 1.0
CB E:ALA21 4.6 26.7 1.0
O E:HOH1015 4.6 23.5 1.0
O E:HOH1006 4.6 15.0 1.0
O E:HOH1044 4.7 29.0 1.0
CA E:ASP24 4.7 24.5 1.0
CB E:ASP24 4.8 23.5 1.0
N E:ASP24 4.9 24.1 1.0

Calcium binding site 10 out of 10 in 1yn8

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Calcium binding site 10 out of 10 in the SH3 Domain of Yeast NBP2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of SH3 Domain of Yeast NBP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1005

b:31.8
occ:1.00
 O E:HOH1052 2.2 38.4 1.0
OE2 E:GLU13 2.3 30.0 1.0
OE2 B:GLU22 2.5 25.5 1.0
O E:HOH1062 2.5 31.8 1.0
O E:HOH1065 2.5 39.4 1.0
OE1 E:GLU13 2.6 22.5 1.0
O B:HOH1047 2.6 35.3 1.0
CD E:GLU13 2.8 23.0 1.0
CA B:CA1004 3.4 29.5 1.0
CD B:GLU22 3.5 28.1 1.0
O E:HOH1063 3.8 42.6 1.0
OE1 B:GLU22 4.1 28.9 1.0
O B:HOH1077 4.2 39.0 1.0
CG E:GLU13 4.3 24.8 1.0
O E:HOH1074 4.3 41.5 1.0
O E:HOH1009 4.5 18.9 1.0
O E:HOH1031 4.6 31.2 1.0
CG B:GLU22 4.7 27.9 1.0
CB B:GLU22 4.8 24.2 1.0
O E:PRO12 4.8 21.5 1.0

Reference:

P.Kursula, I.Kursula, P.Zou, F.Lehmann, Y.H.Song, M.Wilmanns. Structural Analysis of the Yeast SH3 Domain Proteome To Be Published.
Page generated: Sat Dec 12 03:28:55 2020

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