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Calcium in PDB 1rtm: Trimeric Structure of A C-Type Mannose-Binding Protein

Protein crystallography data

The structure of Trimeric Structure of A C-Type Mannose-Binding Protein, PDB code: 1rtm was solved by W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.000, 85.100, 98.500, 90.00, 106.30, 90.00
R / Rfree (%) 22 / 27

Other elements in 1rtm:

The structure of Trimeric Structure of A C-Type Mannose-Binding Protein also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Trimeric Structure of A C-Type Mannose-Binding Protein (pdb code 1rtm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Trimeric Structure of A C-Type Mannose-Binding Protein, PDB code: 1rtm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1rtm

Go back to Calcium Binding Sites List in 1rtm
Calcium binding site 1 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca1

b:18.4
occ:1.00
O 1:HOH235 2.3 15.1 1.0
O 1:GLU193 2.3 20.7 1.0
OD2 1:ASP161 2.3 20.9 1.0
OD1 1:ASP194 2.4 16.5 1.0
OD1 1:ASP188 2.5 17.3 1.0
OE2 1:GLU165 2.5 21.5 1.0
OE1 1:GLU165 2.6 20.1 1.0
OD1 1:ASP161 2.7 21.5 1.0
CG 1:ASP161 2.9 19.5 1.0
CD 1:GLU165 2.9 21.3 1.0
CG 1:ASP188 3.3 19.2 1.0
C 1:GLU193 3.4 17.8 1.0
CG 1:ASP194 3.6 18.9 1.0
CA 1:ASP194 3.8 15.8 1.0
CB 1:ASP188 3.8 18.9 1.0
O 1:HOH234 3.9 22.4 1.0
N 1:ASP194 4.0 15.6 1.0
CA 1:CA3 4.1 20.9 1.0
OD2 1:ASP188 4.2 18.7 1.0
CB 1:ASP194 4.3 18.3 1.0
N 1:GLU193 4.3 20.6 1.0
CB 1:ASP161 4.4 19.2 1.0
CG 1:GLU165 4.4 20.3 1.0
CA 1:ASP188 4.4 22.6 1.0
CA 1:GLU193 4.5 20.0 1.0
CZ 1:PHE168 4.5 21.0 1.0
OD2 1:ASP194 4.6 17.1 1.0
N 1:GLY166 4.7 21.8 1.0
O 1:HOH236 4.7 22.0 1.0
O 1:ASP161 4.7 17.8 1.0
O 1:HOH309 4.8 27.2 1.0
OD2 1:ASP206 4.8 21.6 1.0
O 1:HOH233 4.8 17.0 1.0
C 1:ASP194 5.0 16.0 1.0
CA 1:GLU165 5.0 20.8 1.0

Calcium binding site 2 out of 9 in 1rtm

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Calcium binding site 2 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:23.7
occ:1.00
OD1 1:ASP206 2.2 17.9 1.0
OE1 1:GLU193 2.4 19.4 1.0
OD1 1:ASN205 2.5 14.5 1.0
OD1 1:ASN187 2.5 26.4 1.0
O 1:ASP206 2.5 19.8 1.0
OE1 1:GLU185 2.6 21.3 1.0
O3 1:GOL222 2.6 26.2 1.0
O2 1:GOL222 2.8 32.5 1.0
CG 1:ASP206 3.3 17.8 1.0
CD 1:GLU193 3.4 17.3 1.0
CG 1:ASN205 3.5 12.6 1.0
CG 1:ASN187 3.5 23.1 1.0
CD 1:GLU185 3.5 24.6 1.0
C3 1:GOL222 3.5 33.5 1.0
C 1:ASP206 3.6 21.0 1.0
C2 1:GOL222 3.7 35.2 1.0
N 1:ASP206 3.7 18.8 1.0
OE2 1:GLU193 3.8 20.6 1.0
OE2 1:GLU185 3.8 25.6 1.0
ND2 1:ASN205 3.8 15.9 1.0
OD2 1:ASP206 4.0 21.6 1.0
ND2 1:ASN187 4.0 23.6 1.0
CA 1:ASP206 4.0 16.8 1.0
CB 1:ASP206 4.2 19.4 1.0
N 1:ASN187 4.3 21.4 1.0
CB 1:HIS189 4.4 28.5 1.0
C 1:ASN205 4.6 17.7 1.0
CB 1:ASN187 4.7 25.1 1.0
CG 1:GLU193 4.7 17.8 1.0
N 1:HIS189 4.7 24.8 1.0
N 1:ILE207 4.7 18.8 1.0
CG 1:GLU185 4.7 23.4 1.0
CB 1:ASN205 4.8 16.2 1.0
N 1:ASP188 4.8 22.5 1.0
CA 1:ASN187 4.9 24.4 1.0
CA 1:ASN205 4.9 17.8 1.0
CB 1:GLU193 4.9 18.8 1.0
C1 1:GOL222 5.0 38.4 1.0

Calcium binding site 3 out of 9 in 1rtm

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Calcium binding site 3 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:20.9
occ:1.00
OE1 1:GLU165 2.3 20.1 1.0
O 1:HOH233 2.4 17.0 1.0
O 1:HOH234 2.5 22.4 1.0
OD2 1:ASP194 2.6 17.1 1.0
OD1 1:ASP194 2.7 16.5 1.0
CG 1:ASP194 3.0 18.9 1.0
CD 1:GLU165 3.5 21.3 1.0
CB 1:GLU165 4.1 20.8 1.0
CA 1:CA1 4.1 18.4 1.0
CG 1:GLU165 4.1 20.3 1.0
O 1:HOH285 4.3 21.3 1.0
OD1 1:ASP188 4.4 17.3 1.0
OE2 1:GLU165 4.5 21.5 1.0
O 1:HOH284 4.5 53.1 1.0
CB 1:ASP194 4.5 18.3 1.0
O 1:HOH369 4.5 16.3 1.0
O 1:ASP161 4.6 17.8 1.0
CA 1:GLU165 4.6 20.8 1.0
O 1:HOH232 4.8 27.7 1.0

Calcium binding site 4 out of 9 in 1rtm

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Calcium binding site 4 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca1

b:27.6
occ:1.00
O 2:HOH243 2.3 23.9 1.0
OD1 2:ASP194 2.4 24.0 1.0
OD2 2:ASP161 2.5 28.3 1.0
OE2 2:GLU165 2.5 30.6 1.0
OD1 2:ASP188 2.6 35.1 1.0
O 2:GLU193 2.6 28.6 1.0
OE1 2:GLU165 2.7 28.2 1.0
OD1 2:ASP161 2.7 24.6 1.0
CG 2:ASP161 3.0 27.1 1.0
CD 2:GLU165 3.0 31.6 1.0
CG 2:ASP188 3.4 33.9 1.0
C 2:GLU193 3.5 28.7 1.0
CG 2:ASP194 3.5 26.1 1.0
CA 2:ASP194 3.8 26.6 1.0
CA 2:CA3 3.8 32.6 1.0
CB 2:ASP188 3.9 33.3 1.0
N 2:ASP194 4.0 27.6 1.0
O 2:HOH234 4.1 36.1 1.0
O 2:HOH282 4.2 28.7 1.0
CB 2:ASP194 4.2 26.6 1.0
N 2:GLU193 4.4 31.2 1.0
OD2 2:ASP188 4.4 37.0 1.0
OD2 2:ASP194 4.5 27.3 1.0
CB 2:ASP161 4.5 28.1 1.0
CG 2:GLU165 4.5 32.4 1.0
CA 2:ASP188 4.5 32.8 1.0
CA 2:GLU193 4.5 30.0 1.0
OD2 2:ASP206 4.6 26.0 1.0
CZ 2:PHE168 4.6 28.8 1.0
N 2:GLY166 4.8 29.6 1.0
O 2:ASP161 4.9 28.8 1.0
O 2:HOH233 4.9 28.0 1.0
C 2:ASP194 5.0 25.5 1.0

Calcium binding site 5 out of 9 in 1rtm

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Calcium binding site 5 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:27.7
occ:1.00
OD1 2:ASP206 2.3 29.2 1.0
OE1 2:GLU193 2.3 29.9 1.0
OD1 2:ASN187 2.4 30.2 1.0
O1 2:GOL222 2.5 27.8 1.0
O2 2:GOL222 2.5 36.1 1.0
O 2:ASP206 2.6 27.1 1.0
OD1 2:ASN205 2.7 29.2 1.0
OE1 2:GLU185 2.8 28.6 1.0
C2 2:GOL222 3.3 36.4 1.0
CG 2:ASP206 3.4 29.0 1.0
C1 2:GOL222 3.4 35.9 1.0
CD 2:GLU193 3.4 27.7 1.0
CG 2:ASN187 3.4 34.1 1.0
CD 2:GLU185 3.6 25.9 1.0
C 2:ASP206 3.6 26.6 1.0
CG 2:ASN205 3.7 25.3 1.0
OE2 2:GLU185 3.8 27.0 1.0
OE2 2:GLU193 3.8 28.4 1.0
N 2:ASP206 3.8 22.5 1.0
ND2 2:ASN187 4.0 31.2 1.0
ND2 2:ASN205 4.0 28.2 1.0
OD2 2:ASP206 4.1 26.0 1.0
CA 2:ASP206 4.1 24.8 1.0
N 2:ASN187 4.2 29.2 1.0
CB 2:ASP206 4.3 27.0 1.0
CB 2:HIS189 4.4 37.6 1.0
CB 2:ASN187 4.6 31.4 1.0
N 2:HIS189 4.6 35.2 1.0
N 2:ASP188 4.6 30.7 1.0
C 2:ASN205 4.7 24.4 1.0
CG 2:GLU193 4.7 28.4 1.0
N 2:ILE207 4.7 24.7 1.0
C3 2:GOL222 4.7 38.5 1.0
CA 2:ASN187 4.8 29.6 1.0
CG 2:GLU185 4.8 25.5 1.0
CB 2:GLU193 4.9 29.4 1.0
CB 2:ASN205 4.9 27.3 1.0
C 2:ASN187 5.0 31.6 1.0
O3 2:GOL222 5.0 40.7 1.0

Calcium binding site 6 out of 9 in 1rtm

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Calcium binding site 6 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca3

b:32.6
occ:1.00
OE1 2:GLU165 2.3 28.2 1.0
O 2:HOH233 2.5 28.0 1.0
OD2 2:ASP194 2.5 27.3 1.0
O 2:HOH234 2.5 36.1 1.0
OD1 2:ASP194 2.6 24.0 1.0
CG 2:ASP194 2.9 26.1 1.0
CD 2:GLU165 3.6 31.6 1.0
CA 2:CA1 3.8 27.6 1.0
OD1 2:ASP188 4.0 35.1 1.0
O 2:ASP161 4.3 28.8 1.0
O 2:HOH257 4.4 41.9 1.0
CB 2:ASP194 4.4 26.6 1.0
CB 2:GLU165 4.4 32.5 1.0
CG 2:GLU165 4.5 32.4 1.0
OE2 2:GLU165 4.5 30.6 1.0
OD2 2:ASP161 4.7 28.3 1.0
CA 2:GLU165 4.7 31.0 1.0
OD1 2:ASP161 4.8 24.6 1.0
CG 2:ASP188 4.8 33.9 1.0
OD2 2:ASP188 4.8 37.0 1.0
CG 2:ASP161 4.9 27.1 1.0
O 2:HOH301 5.0 40.0 1.0

Calcium binding site 7 out of 9 in 1rtm

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Calcium binding site 7 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca1

b:22.0
occ:1.00
O 3:GLU193 2.2 20.1 1.0
OD1 3:ASP194 2.3 21.0 1.0
OD2 3:ASP161 2.4 22.3 1.0
OD1 3:ASP188 2.4 22.3 1.0
O 3:HOH238 2.5 22.5 1.0
OE1 3:GLU165 2.6 22.5 1.0
OE2 3:GLU165 2.6 21.9 1.0
OD1 3:ASP161 2.8 21.1 1.0
CG 3:ASP161 2.9 20.8 1.0
CD 3:GLU165 2.9 22.1 1.0
C 3:GLU193 3.2 21.9 1.0
CG 3:ASP188 3.3 21.4 1.0
CG 3:ASP194 3.5 24.9 1.0
CA 3:ASP194 3.7 24.2 1.0
CB 3:ASP188 3.8 22.1 1.0
N 3:ASP194 3.8 22.6 1.0
CA 3:CA3 4.0 25.2 1.0
CB 3:ASP194 4.2 24.2 1.0
N 3:GLU193 4.2 21.3 1.0
OD2 3:ASP188 4.2 24.1 1.0
CA 3:GLU193 4.3 21.0 1.0
CA 3:ASP188 4.4 20.6 1.0
CB 3:ASP161 4.4 23.0 1.0
OD2 3:ASP194 4.4 23.3 1.0
CG 3:GLU165 4.4 22.3 1.0
CZ 3:PHE168 4.5 23.4 1.0
OD2 3:ASP206 4.6 24.8 1.0
O 3:HOH246 4.7 31.5 1.0
N 3:GLY166 4.8 25.9 1.0
O 3:HOH247 4.8 22.2 1.0
O 3:ASP161 4.8 24.4 1.0
C 3:ASP194 4.9 23.2 1.0
CA 3:GLU165 4.9 24.9 1.0

Calcium binding site 8 out of 9 in 1rtm

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Calcium binding site 8 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:23.6
occ:1.00
OD1 3:ASP206 2.3 18.7 1.0
O2 3:GOL222 2.3 26.2 1.0
OE1 3:GLU193 2.4 18.6 1.0
OD1 3:ASN205 2.4 23.9 1.0
OD1 3:ASN187 2.5 21.9 1.0
O 3:ASP206 2.6 24.4 1.0
OE1 3:GLU185 2.6 28.5 1.0
O1 3:GOL222 2.8 23.6 1.0
CG 3:ASP206 3.3 22.3 1.0
CD 3:GLU193 3.4 19.1 1.0
C2 3:GOL222 3.4 31.8 1.0
CG 3:ASN205 3.4 23.3 1.0
CD 3:GLU185 3.4 31.0 1.0
CG 3:ASN187 3.5 24.5 1.0
C1 3:GOL222 3.6 27.8 1.0
C 3:ASP206 3.6 24.3 1.0
N 3:ASP206 3.7 24.1 1.0
OE2 3:GLU185 3.8 30.3 1.0
OE2 3:GLU193 3.8 21.7 1.0
ND2 3:ASN205 3.8 20.3 1.0
OD2 3:ASP206 4.0 24.8 1.0
CA 3:ASP206 4.0 23.1 1.0
ND2 3:ASN187 4.1 20.1 1.0
CB 3:ASP206 4.3 21.7 1.0
N 3:ASN187 4.3 25.7 1.0
C 3:ASN205 4.5 25.5 1.0
CB 3:HIS189 4.6 25.4 1.0
CG 3:GLU193 4.6 20.1 1.0
CG 3:GLU185 4.7 27.7 1.0
C3 3:GOL222 4.7 34.7 1.0
CB 3:ASN205 4.7 23.9 1.0
N 3:ILE207 4.7 22.8 1.0
N 3:HIS189 4.8 22.6 1.0
CB 3:ASN187 4.8 22.9 1.0
CB 3:GLU193 4.8 21.4 1.0
N 3:ASP188 4.8 20.9 1.0
CA 3:ASN205 4.8 24.7 1.0
CA 3:ASN187 4.9 23.0 1.0

Calcium binding site 9 out of 9 in 1rtm

Go back to Calcium Binding Sites List in 1rtm
Calcium binding site 9 out of 9 in the Trimeric Structure of A C-Type Mannose-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Trimeric Structure of A C-Type Mannose-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca3

b:25.2
occ:1.00
OE1 3:GLU165 2.5 22.5 1.0
OD2 3:ASP194 2.5 23.3 1.0
O 3:HOH333 2.6 34.3 1.0
OD1 3:ASP194 2.7 21.0 1.0
CG 3:ASP194 2.9 24.9 1.0
CD 3:GLU165 3.6 22.1 1.0
CA 3:CA1 4.0 22.0 1.0
CB 3:GLU165 4.2 20.1 1.0
OD1 3:ASP188 4.2 22.3 1.0
O 3:HOH235 4.3 23.2 1.0
CG 3:GLU165 4.3 22.3 1.0
CB 3:ASP194 4.4 24.2 1.0
O 3:ASP161 4.5 24.4 1.0
OE2 3:GLU165 4.6 21.9 1.0
CA 3:GLU165 4.6 24.9 1.0
O 3:HOH236 4.6 26.1 1.0
O 3:HOH334 4.7 38.2 1.0
OD2 3:ASP188 4.9 24.1 1.0
O 3:HOH299 4.9 40.4 1.0
OD2 3:ASP161 4.9 22.3 1.0
CG 3:ASP188 4.9 21.4 1.0

Reference:

W.I.Weis, K.Drickamer. Trimeric Structure of A C-Type Mannose-Binding Protein. Structure V. 2 1227 1994.
ISSN: ISSN 0969-2126
PubMed: 7704532
DOI: 10.1016/S0969-2126(94)00124-3
Page generated: Thu Jul 11 22:17:27 2024

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