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Calcium in PDB 1xyd: uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures

Other elements in 1xyd:

The structure of uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures also contains other interesting chemical elements:

Zinc (Zn) 40 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures (pdb code 1xyd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures, PDB code: 1xyd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1xyd

Go back to Calcium Binding Sites List in 1xyd
Calcium binding site 1 out of 4 in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca92

b:0.0
occ:1.00
O A:LYS26 2.1 0.0 1.0
OE2 A:GLU31 2.8 0.0 1.0
O A:GLU21 2.8 0.0 1.0
O A:SER18 2.8 0.0 1.0
HA A:SER18 2.8 0.0 1.0
HG3 A:LYS28 2.9 0.0 1.0
H A:LYS28 2.9 0.0 1.0
HG3 A:GLU21 3.0 0.0 1.0
HA A:LEU27 3.1 0.0 1.0
H A:GLU21 3.1 0.0 1.0
C A:LYS26 3.3 0.0 1.0
C A:SER18 3.4 0.0 1.0
O A:TYR17 3.5 0.0 1.0
N A:LYS28 3.5 0.0 1.0
CA A:SER18 3.6 0.0 1.0
HB2 A:LYS28 3.6 0.0 1.0
C A:GLU21 3.7 0.0 1.0
HG2 A:GLU31 3.8 0.0 1.0
CA A:LEU27 3.8 0.0 1.0
H A:LYS26 3.8 0.0 1.0
CG A:LYS28 3.8 0.0 1.0
CD A:GLU31 3.9 0.0 1.0
CG A:GLU21 3.9 0.0 1.0
N A:GLU21 3.9 0.0 1.0
C A:LEU27 4.0 0.0 1.0
N A:LEU27 4.0 0.0 1.0
HG2 A:GLU21 4.0 0.0 1.0
HA3 A:GLY22 4.1 0.0 1.0
CB A:LYS28 4.1 0.0 1.0
HB3 A:LYS26 4.1 0.0 1.0
HD2 A:LYS28 4.2 0.0 1.0
HD23 A:LEU27 4.2 0.0 1.0
H A:ARG20 4.2 0.0 1.0
HE2 A:LYS28 4.2 0.0 1.0
HB3 A:ARG20 4.2 0.0 1.0
C A:TYR17 4.3 0.0 1.0
CA A:GLU21 4.4 0.0 1.0
CG A:GLU31 4.4 0.0 1.0
CA A:LYS26 4.4 0.0 1.0
HZ2 A:LYS28 4.4 0.0 1.0
N A:SER18 4.4 0.0 1.0
N A:LYS26 4.5 0.0 1.0
CA A:LYS28 4.5 0.0 1.0
N A:GLY19 4.5 0.0 1.0
CD A:LYS28 4.5 0.0 1.0
HB2 A:SER18 4.5 0.0 1.0
HG2 A:LYS28 4.6 0.0 1.0
N A:ARG20 4.7 0.0 1.0
HD22 A:LEU27 4.7 0.0 1.0
N A:GLY22 4.7 0.0 1.0
CB A:SER18 4.7 0.0 1.0
CB A:GLU21 4.7 0.0 1.0
CE A:LYS28 4.8 0.0 1.0
CB A:LYS26 4.8 0.0 1.0
HB2 A:GLU31 4.9 0.0 1.0
OE1 A:GLU31 4.9 0.0 1.0
HA2 A:GLY19 4.9 0.0 1.0
CA A:GLY22 4.9 0.0 1.0
CD2 A:LEU27 4.9 0.0 1.0
H A:LEU27 4.9 0.0 1.0
CD A:GLU21 5.0 0.0 1.0

Calcium binding site 2 out of 4 in 1xyd

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Calcium binding site 2 out of 4 in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca93

b:0.0
occ:1.00
OE2 A:GLU72 2.2 0.0 1.0
O A:GLU67 2.4 0.0 1.0
OE1 A:GLU72 2.4 0.0 1.0
OD2 A:ASP65 2.4 0.0 1.0
CD A:GLU72 2.5 0.0 1.0
OD1 A:ASP65 2.5 0.0 1.0
OD1 A:ASP61 2.6 0.0 1.0
CG A:ASP65 2.7 0.0 1.0
HA A:CYS68 2.8 0.0 1.0
OD1 A:ASP63 2.9 0.0 1.0
HA A:ASP61 3.0 0.0 1.0
H A:ASP69 3.1 0.0 1.0
OD2 A:ASP63 3.4 0.0 1.0
C A:GLU67 3.4 0.0 1.0
CG A:ASP63 3.5 0.0 1.0
CG A:ASP61 3.5 0.0 1.0
H A:GLU62 3.6 0.0 1.0
H A:ASP65 3.6 0.0 1.0
CA A:CYS68 3.7 0.0 1.0
H A:ASP63 3.8 0.0 1.0
CG A:GLU72 3.9 0.0 1.0
H A:GLU67 3.9 0.0 1.0
CA A:ASP61 4.0 0.0 1.0
N A:CYS68 4.0 0.0 1.0
N A:ASP69 4.0 0.0 1.0
HG3 A:GLU72 4.0 0.0 1.0
CB A:ASP65 4.1 0.0 1.0
OD2 A:ASP61 4.2 0.0 1.0
CB A:ASP61 4.3 0.0 1.0
HG2 A:GLU72 4.3 0.0 1.0
N A:GLU62 4.3 0.0 1.0
HB3 A:ASP65 4.3 0.0 1.0
HB2 A:GLU67 4.4 0.0 1.0
C A:CYS68 4.4 0.0 1.0
OD2 A:ASP69 4.4 0.0 1.0
N A:GLU67 4.5 0.0 1.0
N A:ASP65 4.5 0.0 1.0
HB2 A:ASP61 4.5 0.0 1.0
CA A:GLU67 4.5 0.0 1.0
H A:GLY64 4.5 0.0 1.0
C A:ASP61 4.6 0.0 1.0
N A:ASP63 4.7 0.0 1.0
H A:GLY66 4.7 0.0 1.0
CG A:ASP69 4.7 0.0 1.0
SG A:CYS68 4.8 0.0 1.0
HB2 A:ASP65 4.8 0.0 1.0
HB3 A:ASP69 4.8 0.0 1.0
HB3 A:GLU72 4.8 0.0 1.0
CA A:ASP65 4.9 0.0 1.0
CB A:CYS68 4.9 0.0 1.0
H A:CYS68 4.9 0.0 1.0
CB A:ASP63 4.9 0.0 1.0
CB A:GLU72 4.9 0.0 1.0

Calcium binding site 3 out of 4 in 1xyd

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Calcium binding site 3 out of 4 in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca92

b:0.0
occ:1.00
H B:GLU21 2.4 0.0 1.0
O B:GLU21 2.4 0.0 1.0
O B:SER18 2.4 0.0 1.0
O B:LYS26 2.6 0.0 1.0
HG3 B:GLU21 2.8 0.0 1.0
OE2 B:GLU31 2.8 0.0 1.0
HA B:SER18 2.9 0.0 1.0
C B:SER18 3.0 0.0 1.0
O B:TYR17 3.0 0.0 1.0
N B:GLU21 3.3 0.0 1.0
C B:GLU21 3.3 0.0 1.0
CA B:SER18 3.4 0.0 1.0
HG3 B:LYS28 3.5 0.0 1.0
H B:LYS28 3.5 0.0 1.0
H B:ARG20 3.6 0.0 1.0
HA B:LEU27 3.6 0.0 1.0
HG2 B:GLU21 3.6 0.0 1.0
CG B:GLU21 3.6 0.0 1.0
HB3 B:ARG20 3.7 0.0 1.0
HG2 B:GLU31 3.7 0.0 1.0
CA B:GLU21 3.8 0.0 1.0
C B:LYS26 3.8 0.0 1.0
H B:LYS26 3.9 0.0 1.0
CD B:GLU31 3.9 0.0 1.0
N B:ARG20 3.9 0.0 1.0
N B:GLY19 4.0 0.0 1.0
C B:TYR17 4.0 0.0 1.0
HB2 B:LYS28 4.0 0.0 1.0
HA3 B:GLY22 4.1 0.0 1.0
N B:LYS28 4.2 0.0 1.0
N B:SER18 4.2 0.0 1.0
HA2 B:GLY19 4.3 0.0 1.0
C B:ARG20 4.4 0.0 1.0
CB B:GLU21 4.4 0.0 1.0
C B:GLY19 4.4 0.0 1.0
CG B:LYS28 4.4 0.0 1.0
CG B:GLU31 4.4 0.0 1.0
HD2 B:LYS28 4.4 0.0 1.0
HE2 B:LYS28 4.4 0.0 1.0
CA B:LEU27 4.4 0.0 1.0
N B:GLY22 4.4 0.0 1.0
CA B:GLY19 4.5 0.0 1.0
HD23 B:LEU27 4.5 0.0 1.0
CA B:ARG20 4.6 0.0 1.0
HB3 B:LYS26 4.6 0.0 1.0
CB B:ARG20 4.6 0.0 1.0
N B:LEU27 4.6 0.0 1.0
HB2 B:SER18 4.6 0.0 1.0
H B:GLY19 4.6 0.0 1.0
N B:LYS26 4.7 0.0 1.0
CB B:LYS28 4.7 0.0 1.0
CB B:SER18 4.7 0.0 1.0
C B:LEU27 4.7 0.0 1.0
HA B:GLU21 4.8 0.0 1.0
HB2 B:GLU21 4.8 0.0 1.0
CA B:GLY22 4.8 0.0 1.0
CA B:LYS26 4.8 0.0 1.0
CD B:LYS28 4.9 0.0 1.0
CD B:GLU21 4.9 0.0 1.0
OE1 B:GLU31 5.0 0.0 1.0
HD22 B:LEU27 5.0 0.0 1.0

Calcium binding site 4 out of 4 in 1xyd

Go back to Calcium Binding Sites List in 1xyd
Calcium binding site 4 out of 4 in the uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of uc(Nmr) Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca93

b:0.0
occ:1.00
OD1 B:ASP61 2.1 0.0 1.0
OD1 B:ASP65 2.2 0.0 1.0
OD1 B:ASP63 2.3 0.0 1.0
OD2 B:ASP65 2.4 0.0 1.0
CG B:ASP65 2.5 0.0 1.0
OE1 B:GLU72 2.6 0.0 1.0
O B:GLU67 2.7 0.0 1.0
OE2 B:GLU72 2.8 0.0 1.0
HA B:ASP61 2.9 0.0 1.0
H B:ASP65 3.0 0.0 1.0
CD B:GLU72 3.0 0.0 1.0
CG B:ASP63 3.0 0.0 1.0
CG B:ASP61 3.0 0.0 1.0
OD2 B:ASP63 3.1 0.0 1.0
H B:ASP63 3.4 0.0 1.0
H B:GLU62 3.4 0.0 1.0
HA B:CYS68 3.4 0.0 1.0
H B:ASP69 3.7 0.0 1.0
H B:GLU67 3.8 0.0 1.0
CB B:ASP65 3.8 0.0 1.0
C B:GLU67 3.8 0.0 1.0
OD2 B:ASP61 3.8 0.0 1.0
CA B:ASP61 3.8 0.0 1.0
N B:ASP65 3.9 0.0 1.0
HB3 B:ASP65 3.9 0.0 1.0
H B:GLY64 3.9 0.0 1.0
CB B:ASP61 4.0 0.0 1.0
N B:GLU62 4.0 0.0 1.0
N B:ASP63 4.2 0.0 1.0
H B:GLY66 4.3 0.0 1.0
C B:ASP61 4.3 0.0 1.0
HB2 B:ASP61 4.3 0.0 1.0
CA B:CYS68 4.4 0.0 1.0
CA B:ASP65 4.4 0.0 1.0
N B:GLY64 4.4 0.0 1.0
CG B:GLU72 4.4 0.0 1.0
CB B:ASP63 4.4 0.0 1.0
N B:GLU67 4.5 0.0 1.0
N B:CYS68 4.5 0.0 1.0
HB2 B:ASP65 4.6 0.0 1.0
HG3 B:GLU72 4.6 0.0 1.0
HB2 B:GLU67 4.6 0.0 1.0
N B:ASP69 4.6 0.0 1.0
CA B:ASP63 4.7 0.0 1.0
CA B:GLU67 4.7 0.0 1.0
N B:GLY66 4.7 0.0 1.0
OD2 B:ASP69 4.8 0.0 1.0
C B:ASP63 4.8 0.0 1.0
C B:ASP65 4.8 0.0 1.0
HB3 B:ASP61 4.9 0.0 1.0
HG2 B:GLU72 4.9 0.0 1.0
C B:GLY64 4.9 0.0 1.0
HB3 B:ASP63 5.0 0.0 1.0
N B:ASP61 5.0 0.0 1.0

Reference:

P.T.Wilder, K.M.Varney, M.B.Weiss, R.K.Gitti, D.J.Weber. Solution Structure of Zinc- and Calcium-Bound Rat S100B As Determined By Nuclear Magnetic Resonance Spectroscopy Biochemistry V. 44 5690 2005.
ISSN: ISSN 0006-2960
PubMed: 15823027
DOI: 10.1021/BI0475830
Page generated: Sat Dec 12 03:27:48 2020

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