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Calcium in PDB 2iwv: Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation

Protein crystallography data

The structure of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation, PDB code: 2iwv was solved by O.Yildiz, K.R.Vinothkumar, P.Goswami, W.Kuehlbrandt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 2.3
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.600, 77.000, 103.900, 79.30, 73.40, 74.30
R / Rfree (%) 22.4 / 26.9

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Calcium atom in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation (pdb code 2iwv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 33 binding sites of Calcium where determined in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation, PDB code: 2iwv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 33 in 2iwv

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Calcium binding site 1 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca311

b:90.4
occ:1.00
 O A:HOH2009 2.7 55.3 1.0
OG A:SER58 3.6 48.6 1.0
CB A:SER58 4.4 44.6 1.0
OD2 A:ASP56 4.5 59.4 1.0
OD1 A:ASP27 4.6 48.9 1.0
OD2 A:ASP27 4.6 49.8 1.0

Calcium binding site 2 out of 33 in 2iwv

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Calcium binding site 2 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1281

b:49.3
occ:1.00
 O A:HOH2006 1.8 52.7 1.0
OD2 A:ASP25 2.3 57.4 1.0
O A:MET26 2.3 51.0 1.0
O A:GLY21 2.4 48.4 1.0
O A:VAL19 2.5 47.9 1.0
OD1 A:ASN18 2.5 35.0 1.0
O A:HOH2008 2.6 40.0 1.0
C A:MET26 3.4 50.7 1.0
CG A:ASP25 3.5 58.1 1.0
CG A:ASN18 3.5 40.5 1.0
C A:VAL19 3.6 46.5 1.0
C A:GLY21 3.6 48.0 1.0
O A:ASP25 3.7 63.9 1.0
N A:GLY28 3.9 44.6 1.0
OD1 A:ASP25 4.1 56.3 1.0
ND2 A:ASN18 4.1 43.2 1.0
N A:VAL19 4.1 40.9 1.0
C A:ASP25 4.1 59.0 1.0
C A:ASP27 4.1 46.1 1.0
N A:GLY23 4.2 57.0 1.0
N A:ASP27 4.2 48.3 1.0
CA A:ASP27 4.3 46.4 1.0
CA A:CA1282 4.3 96.4 1.0
N A:GLY21 4.4 45.5 1.0
CA A:MET26 4.4 52.9 1.0
CA A:GLU20 4.4 46.6 1.0
CA A:TYR22 4.4 52.1 1.0
CA A:VAL19 4.4 42.4 1.0
N A:TYR22 4.5 50.2 1.0
C A:GLU20 4.5 46.2 1.0
N A:GLU20 4.5 45.8 1.0
CA A:GLY28 4.6 41.0 1.0
CA A:GLY21 4.6 45.6 1.0
CB A:ASN18 4.7 39.5 1.0
N A:MET26 4.7 55.3 1.0
CB A:ASP25 4.7 58.6 1.0
O A:ASP27 4.7 48.8 1.0
C A:ASN18 4.8 40.7 1.0
CB A:VAL19 4.8 40.8 1.0
CA A:ASP25 4.8 59.4 1.0
CA A:ASN18 4.9 39.1 1.0
C A:TYR22 4.9 54.7 1.0
N A:ASP25 5.0 61.7 1.0

Calcium binding site 3 out of 33 in 2iwv

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Calcium binding site 3 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1282

b:96.4
occ:1.00
 O A:HOH2102 2.6 67.2 1.0
O A:GLU20 2.8 48.1 1.0
O A:HOH2008 2.8 40.0 1.0
O A:VAL19 3.2 47.9 1.0
C A:GLU20 3.4 46.2 1.0
O A:GLY21 3.4 48.4 1.0
C A:GLY21 3.5 48.0 1.0
CG1 A:VAL19 3.5 40.9 1.0
CA A:GLY21 3.5 45.6 1.0
N A:GLY23 3.6 57.0 1.0
CA A:GLY23 3.8 58.5 1.0
C A:VAL19 3.8 46.5 1.0
N A:GLY21 3.8 45.5 1.0
CB A:VAL19 3.9 40.8 1.0
N A:TYR22 4.2 50.2 1.0
N A:GLU20 4.3 45.8 1.0
CA A:CA1281 4.3 49.3 1.0
CA A:GLU20 4.4 46.6 1.0
CA A:VAL19 4.5 42.4 1.0
C A:TYR22 4.6 54.7 1.0
OD1 A:ASP267 4.8 58.4 1.0
CA A:TYR22 4.9 52.1 1.0
C A:GLY23 4.9 59.8 1.0

Calcium binding site 4 out of 33 in 2iwv

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Calcium binding site 4 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1283

b:49.5
occ:1.00
 OE2 A:GLU229 1.8 55.5 1.0
OD2 A:ASP221 2.0 51.4 1.0
OD2 A:ASP225 2.1 63.2 1.0
ND2 A:ASN219 2.2 39.9 1.0
O A:GLU227 2.2 50.8 1.0
O A:ASP225 2.4 52.5 1.0
CD A:GLU229 2.7 56.2 1.0
OE1 A:GLU229 2.9 63.3 1.0
CG A:ASP221 3.1 51.1 1.0
CG A:ASP225 3.2 60.8 1.0
CG A:ASN219 3.4 44.4 1.0
C A:ASP225 3.5 52.1 1.0
C A:GLU227 3.5 50.2 1.0
OD1 A:ASP221 3.5 50.7 1.0
CB A:ASP225 3.8 56.2 1.0
CA A:CA1284 3.9 67.0 1.0
CG A:GLU229 4.1 51.5 1.0
OD1 A:ASN219 4.1 47.6 1.0
CA A:ASP225 4.2 54.9 1.0
OD1 A:ASP225 4.2 62.1 1.0
N A:GLU227 4.2 48.5 1.0
C A:ASP221 4.3 50.6 1.0
N A:ARG228 4.4 48.0 1.0
N A:TRP222 4.4 50.5 1.0
C A:ILE226 4.4 49.0 1.0
O A:HOH2084 4.4 53.0 1.0
CA A:ASN219 4.4 46.0 1.0
CA A:GLU227 4.4 52.5 1.0
CB A:ASP221 4.4 48.4 1.0
N A:ILE226 4.5 51.4 1.0
O A:ASP221 4.5 51.6 1.0
CB A:ASN219 4.5 45.5 1.0
CA A:ARG228 4.5 45.0 1.0
CA A:TRP222 4.6 49.9 1.0
N A:GLU229 4.6 46.5 1.0
C A:ARG228 4.6 46.3 1.0
N A:ASP221 4.7 51.1 1.0
CA A:ASP221 4.7 49.9 1.0
CA A:ILE226 4.8 50.2 1.0
O A:ILE226 4.8 50.0 1.0
O A:HOH2098 4.9 46.5 1.0
C A:ASN219 4.9 48.6 1.0

Calcium binding site 5 out of 33 in 2iwv

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Calcium binding site 5 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1284

b:67.0
occ:1.00
 O A:HOH2084 2.0 53.0 1.0
O A:HOH2098 2.0 46.5 1.0
OE1 A:GLU229 2.3 63.3 1.0
OD2 A:ASP225 2.4 63.2 1.0
CG A:ASP225 3.0 60.8 1.0
OD1 A:ASP225 3.0 62.1 1.0
OE2 A:GLU263 3.4 20.0 1.0
CD A:GLU229 3.5 56.2 1.0
CA A:CA1283 3.9 49.5 1.0
CD A:GLU263 3.9 20.0 1.0
OE2 A:GLU229 4.1 55.5 1.0
OD1 A:ASP221 4.2 50.7 1.0
CB A:ASP225 4.3 56.2 1.0
O A:GLU227 4.4 50.8 1.0
CG A:GLU263 4.5 20.0 1.0
OE1 A:GLU263 4.6 20.0 1.0
CG A:GLU229 4.6 51.5 1.0
OD2 A:ASP221 4.8 51.4 1.0
CB A:GLU229 4.9 45.8 1.0
CG A:ASP221 5.0 51.1 1.0

Calcium binding site 6 out of 33 in 2iwv

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Calcium binding site 6 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1285

b:76.2
occ:1.00
 O A:HOH2101 1.7 52.5 1.0
O A:HIS261 2.2 55.7 1.0
O A:HOH2100 2.3 62.9 1.0
O A:HOH2096 3.0 71.0 1.0
C A:HIS261 3.4 54.8 1.0
O A:GLY264 3.7 64.8 1.0
N A:HIS261 4.1 50.3 1.0
CA A:HIS261 4.3 50.8 1.0
N A:ASP262 4.4 56.4 1.0
CA A:ASP262 4.5 59.3 1.0
CB A:ASP260 4.6 58.1 1.0
O A:ASP262 4.6 63.0 1.0
OG A:SER266 4.6 57.7 1.0
C A:ASP262 4.7 62.3 1.0
C A:ASP260 4.7 52.3 1.0
C A:GLY264 4.8 64.5 1.0
CA A:ASP260 4.9 53.7 1.0

Calcium binding site 7 out of 33 in 2iwv

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Calcium binding site 7 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1286

b:0.6
occ:1.00
 O A:ARG216 3.4 42.3 1.0
OD2 A:ASP215 3.4 63.0 1.0
CA A:GLY230 3.7 43.5 1.0
N A:HIS231 3.9 43.9 1.0
O A:HIS231 4.2 48.5 1.0
C A:GLY230 4.2 44.7 1.0
N A:ARG216 4.3 45.1 1.0
O A:HOH2032 4.3 65.7 1.0
C A:ARG216 4.4 40.7 1.0
OD2 A:ASP262 4.4 62.9 1.0
CG A:ASP215 4.5 59.6 1.0
N A:GLY230 4.9 44.2 1.0
CA A:ARG216 5.0 40.0 1.0

Calcium binding site 8 out of 33 in 2iwv

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Calcium binding site 8 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1287

b:0.9
occ:1.00
 O B:HOH2096 2.7 79.3 1.0
OD1 B:ASP224 2.7 72.3 1.0
O A:HOH2077 2.9 77.1 1.0
OD1 A:ASP243 3.0 64.3 1.0
CB A:ASP243 3.6 48.0 1.0
CG A:ASP243 3.8 56.8 1.0
CG B:ASP224 4.0 69.9 1.0
O A:GLY202 4.1 51.5 1.0
OD1 A:ASN203 4.5 56.1 1.0
O B:GLN223 4.5 57.8 1.0
CA A:ASN203 4.6 50.5 1.0
CB B:ASP224 4.8 65.3 1.0
OD2 B:ASP224 4.8 71.5 1.0
CA B:ASP224 4.8 62.1 1.0
O A:ASN203 4.9 46.6 1.0
C A:ASN203 4.9 47.8 1.0
C A:GLY202 5.0 51.4 1.0
OD2 A:ASP243 5.0 58.9 1.0

Calcium binding site 9 out of 33 in 2iwv

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Calcium binding site 9 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1288

b:0.1
occ:1.00
 OE1 A:GLU17 3.0 49.5 1.0
OE2 A:GLU52 3.4 58.2 1.0
OE2 A:GLU17 3.6 50.5 1.0
CD A:GLU17 3.7 48.8 1.0
OH A:TYR50 3.9 41.1 1.0
OE2 A:GLU31 4.1 39.6 1.0
CD A:GLU52 4.2 51.8 1.0
OE1 A:GLU31 4.4 47.9 1.0
OE1 A:GLU52 4.5 55.6 1.0
CD A:GLU31 4.6 41.1 1.0

Calcium binding site 10 out of 33 in 2iwv

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Calcium binding site 10 out of 33 in the Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Monomeric Outer Membrane Porin Ompg in the Open and Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca313

b:0.5
occ:1.00
 OG B:SER279 4.0 60.5 1.0
CB B:SER279 4.6 54.1 1.0

Reference:

O.Yildiz, K.R.Vinothkumar, P.Goswami, W.Kuhlbrandt. Structure of the Monomeric Outer-Membrane Porin Ompg in the Open and Closed Conformation. Embo J. V. 25 3702 2006.
ISSN: ISSN 0261-4189
PubMed: 16888630
DOI: 10.1038/SJ.EMBOJ.7601237
Page generated: Fri Jul 12 13:11:27 2024

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