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Calcium in PDB 6ih1: Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form

Enzymatic activity of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form

All present enzymatic activity of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form:
3.1.4.52;

Protein crystallography data

The structure of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form, PDB code: 6ih1 was solved by M.Yadav, K.Pal, U.Sen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.92 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.500, 42.630, 156.340, 90.00, 94.42, 90.00
R / Rfree (%) 18.3 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form (pdb code 6ih1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form, PDB code: 6ih1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ih1

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Calcium binding site 1 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:29.7
occ:1.00
 OE2 A:GLU128 2.1 34.9 1.0
O A:HOH601 2.3 22.6 1.0
OD1 A:ASN95 2.3 34.1 1.0
OE2 A:GLU45 2.3 32.5 1.0
OD2 A:ASP158 2.4 34.3 1.0
O2P A:C2E501 2.4 45.4 1.0
CG A:ASP158 3.2 30.0 1.0
CD A:GLU45 3.3 33.6 1.0
CD A:GLU128 3.3 33.6 1.0
CG A:ASN95 3.3 39.1 1.0
OD1 A:ASP158 3.5 29.9 1.0
P1 A:C2E501 3.6 48.4 1.0
OE1 A:GLU45 3.7 28.1 1.0
ND2 A:ASN95 3.7 39.6 1.0
CA A:CA503 3.8 72.9 1.0
O5' A:C2E501 4.0 50.3 1.0
OE1 A:GLU128 4.1 30.6 1.0
O1P A:C2E501 4.1 46.5 1.0
NZ A:LYS179 4.1 22.5 1.0
CB A:GLU128 4.2 33.1 1.0
O A:HOH603 4.3 40.6 1.0
CG A:GLU128 4.3 31.4 1.0
CB A:ASP158 4.3 26.4 1.0
OE1 A:GLU215 4.4 52.9 1.0
CG A:GLU45 4.5 31.7 1.0
CB A:ASN95 4.7 38.6 1.0
CD A:LYS179 4.9 19.9 1.0

Calcium binding site 2 out of 8 in 6ih1

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Calcium binding site 2 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:72.9
occ:1.00
 OD1 A:ASP159 2.3 36.5 1.0
O1P A:C2E501 2.3 46.5 1.0
OE2 A:GLU215 2.3 45.1 1.0
OD1 A:ASP158 2.4 29.9 1.0
O A:HOH601 2.9 22.6 1.0
CD A:GLU215 2.9 48.1 1.0
OE1 A:GLU215 3.0 52.9 1.0
CG A:ASP158 3.1 30.0 1.0
OD2 A:ASP158 3.1 34.3 1.0
CG A:ASP159 3.2 37.2 1.0
O2P A:C2E501 3.4 45.4 1.0
P1 A:C2E501 3.4 48.4 1.0
O A:HOH603 3.6 40.6 1.0
OD2 A:ASP159 3.7 40.2 1.0
CA A:CA502 3.8 29.7 1.0
O A:HOH659 3.9 36.1 1.0
N A:ASP159 3.9 24.0 1.0
O5' A:C2E501 4.2 50.3 1.0
CG A:GLU215 4.3 44.5 1.0
CA A:ASP159 4.3 27.3 1.0
CB A:ASP159 4.4 33.3 1.0
C5' A:C2E501 4.4 51.2 1.0
CB A:ASP158 4.4 26.4 1.0
O3A A:C2E501 4.6 53.7 1.0
C A:ASP158 4.8 26.1 1.0
CA A:ASP158 4.9 25.1 1.0

Calcium binding site 3 out of 8 in 6ih1

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Calcium binding site 3 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:26.7
occ:1.00
 OE2 B:GLU128 2.2 22.5 1.0
OE2 B:GLU45 2.3 25.8 1.0
O2P B:C2E501 2.3 46.8 1.0
O B:HOH602 2.3 21.5 1.0
OD2 B:ASP158 2.3 31.3 1.0
OD1 B:ASN95 2.3 27.7 1.0
CG B:ASP158 3.2 28.6 1.0
CD B:GLU45 3.2 26.5 1.0
CG B:ASN95 3.4 29.1 1.0
CD B:GLU128 3.4 23.7 1.0
P1 B:C2E501 3.5 42.1 1.0
OD1 B:ASP158 3.6 25.1 1.0
OE1 B:GLU45 3.6 25.9 1.0
CA B:CA503 3.7 77.7 1.0
ND2 B:ASN95 3.7 28.1 1.0
O5' B:C2E501 3.9 35.2 1.0
O1P B:C2E501 3.9 57.2 1.0
O B:HOH660 4.1 43.8 1.0
NZ B:LYS179 4.1 19.4 1.0
OE1 B:GLU128 4.1 21.7 1.0
CB B:GLU128 4.3 21.0 1.0
OE1 B:GLU215 4.3 41.2 1.0
CB B:ASP158 4.4 27.4 1.0
CG B:GLU128 4.4 24.1 1.0
CG B:GLU45 4.4 25.9 1.0
CB B:ASN95 4.7 31.8 1.0
CD B:LYS179 4.9 20.4 1.0
O3A B:C2E501 4.9 42.1 1.0
C5' B:C2E501 5.0 35.5 1.0

Calcium binding site 4 out of 8 in 6ih1

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Calcium binding site 4 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:77.7
occ:1.00
 O1P B:C2E501 2.2 57.2 1.0
OD1 B:ASP159 2.4 32.9 1.0
OE2 B:GLU215 2.4 40.5 1.0
OD1 B:ASP158 2.5 25.1 1.0
O B:HOH602 2.7 21.5 1.0
OE1 B:GLU215 2.9 41.2 1.0
CD B:GLU215 2.9 39.6 1.0
OD2 B:ASP158 3.0 31.3 1.0
CG B:ASP158 3.0 28.6 1.0
CG B:ASP159 3.3 35.0 1.0
P1 B:C2E501 3.3 42.1 1.0
O2P B:C2E501 3.4 46.8 1.0
CA B:CA502 3.7 26.7 1.0
O B:HOH658 3.8 29.3 1.0
OD2 B:ASP159 3.8 39.5 1.0
O B:HOH660 3.9 43.8 1.0
N B:ASP159 4.0 24.4 1.0
O5' B:C2E501 4.1 35.2 1.0
O B:HOH676 4.1 39.3 1.0
CG B:GLU215 4.3 40.8 1.0
C5' B:C2E501 4.3 35.5 1.0
CA B:ASP159 4.4 25.5 1.0
CB B:ASP159 4.4 30.1 1.0
CB B:ASP158 4.4 27.4 1.0
O3A B:C2E501 4.6 42.1 1.0
C B:ASP158 4.8 25.1 1.0
CA B:ASP158 4.9 22.5 1.0
OE2 B:GLU128 5.0 22.5 1.0

Calcium binding site 5 out of 8 in 6ih1

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Calcium binding site 5 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:20.2
occ:1.00
 OE2 C:GLU128 2.2 24.2 1.0
O2P C:C2E501 2.2 31.4 1.0
OE2 C:GLU45 2.2 24.9 1.0
OD1 C:ASN95 2.3 27.2 1.0
OD2 C:ASP158 2.3 24.4 1.0
O C:HOH615 2.3 20.1 1.0
CG C:ASP158 3.1 21.6 1.0
CD C:GLU45 3.3 25.3 1.0
CG C:ASN95 3.3 30.9 1.0
CD C:GLU128 3.3 24.9 1.0
CA C:CA503 3.5 76.9 1.0
P1 C:C2E501 3.6 31.1 1.0
OD1 C:ASP158 3.6 22.8 1.0
ND2 C:ASN95 3.7 27.5 1.0
OE1 C:GLU45 3.7 24.1 1.0
O5' C:C2E501 4.1 30.9 1.0
NZ C:LYS179 4.1 14.3 1.0
OE1 C:GLU128 4.1 20.1 1.0
O1P C:C2E501 4.1 29.0 1.0
CB C:GLU128 4.2 24.0 1.0
CB C:ASP158 4.2 21.9 1.0
O C:HOH641 4.2 36.0 1.0
CG C:GLU128 4.4 23.9 1.0
CG C:GLU45 4.5 19.4 1.0
OE1 C:GLU215 4.6 40.5 1.0
CB C:ASN95 4.7 32.2 1.0
CD C:LYS179 4.9 21.9 1.0
O3A C:C2E501 5.0 32.2 1.0
CE C:LYS179 5.0 25.4 1.0

Calcium binding site 6 out of 8 in 6ih1

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Calcium binding site 6 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:76.9
occ:1.00
 OD1 C:ASP158 2.3 22.8 1.0
O1P C:C2E501 2.3 29.0 1.0
OD1 C:ASP159 2.4 31.1 1.0
OE2 C:GLU215 2.4 40.9 1.0
OD2 C:ASP158 2.6 24.4 1.0
O C:HOH615 2.6 20.1 1.0
CG C:ASP158 2.7 21.6 1.0
O2P C:C2E501 3.0 31.4 1.0
CD C:GLU215 3.1 38.2 1.0
OE1 C:GLU215 3.2 40.5 1.0
P1 C:C2E501 3.2 31.1 1.0
CG C:ASP159 3.3 31.4 1.0
CA C:CA502 3.5 20.2 1.0
O C:HOH641 3.7 36.0 1.0
OD2 C:ASP159 3.7 38.2 1.0
N C:ASP159 3.9 19.9 1.0
O C:HOH613 4.0 30.0 1.0
CB C:ASP158 4.1 21.9 1.0
O5' C:C2E501 4.2 30.9 1.0
CA C:ASP159 4.4 21.1 1.0
CB C:ASP159 4.4 23.6 1.0
C5' C:C2E501 4.5 37.2 1.0
O3A C:C2E501 4.5 32.2 1.0
CG C:GLU215 4.6 37.4 1.0
C C:ASP158 4.7 21.2 1.0
CA C:ASP158 4.7 19.2 1.0
OE2 C:GLU128 4.8 24.2 1.0

Calcium binding site 7 out of 8 in 6ih1

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Calcium binding site 7 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:27.2
occ:1.00
 OE2 D:GLU128 2.2 25.4 1.0
O2P D:C2E501 2.3 38.9 1.0
O D:HOH603 2.3 21.2 1.0
OD2 D:ASP158 2.4 27.8 1.0
OD1 D:ASN95 2.4 25.0 1.0
OE2 D:GLU45 2.4 23.9 1.0
CG D:ASP158 3.1 23.8 1.0
CD D:GLU45 3.3 24.0 1.0
CD D:GLU128 3.4 24.8 1.0
CG D:ASN95 3.4 26.6 1.0
OD1 D:ASP158 3.6 25.5 1.0
P1 D:C2E501 3.6 38.7 1.0
CA D:CA503 3.6 96.2 1.0
OE1 D:GLU45 3.7 24.4 1.0
ND2 D:ASN95 3.8 23.7 1.0
O1P D:C2E501 4.0 54.0 1.0
O5' D:C2E501 4.1 32.9 1.0
O D:HOH639 4.1 33.8 1.0
NZ D:LYS179 4.1 21.5 1.0
OE1 D:GLU128 4.2 23.4 1.0
CB D:ASP158 4.3 24.2 1.0
CB D:GLU128 4.3 26.5 1.0
OE2 D:GLU215 4.4 62.5 1.0
CG D:GLU128 4.4 25.8 1.0
CG D:GLU45 4.6 20.4 1.0
CB D:ASN95 4.7 29.0 1.0
CD D:LYS179 4.9 20.0 1.0
O3A D:C2E501 5.0 36.9 1.0
CE D:LYS179 5.0 19.6 1.0

Calcium binding site 8 out of 8 in 6ih1

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Calcium binding site 8 out of 8 in the Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:96.2
occ:1.00
 OD1 D:ASP158 2.3 25.5 1.0
O1P D:C2E501 2.4 54.0 1.0
OD1 D:ASP159 2.4 33.5 1.0
OE2 D:GLU215 2.5 62.5 1.0
OE1 D:GLU215 2.6 58.3 1.0
O D:HOH603 2.6 21.2 1.0
OD2 D:ASP158 2.7 27.8 1.0
CG D:ASP158 2.7 23.8 1.0
CD D:GLU215 2.9 55.1 1.0
CG D:ASP159 3.3 35.9 1.0
O2P D:C2E501 3.4 38.9 1.0
P1 D:C2E501 3.5 38.7 1.0
CA D:CA502 3.6 27.2 1.0
OD2 D:ASP159 3.8 40.4 1.0
N D:ASP159 3.8 23.8 1.0
O D:HOH639 4.0 33.8 1.0
O D:HOH654 4.0 26.4 1.0
CB D:ASP158 4.1 24.2 1.0
O5' D:C2E501 4.3 32.9 1.0
CA D:ASP159 4.3 23.7 1.0
CG D:GLU215 4.4 47.8 1.0
CB D:ASP159 4.4 29.0 1.0
O D:HOH681 4.4 45.4 1.0
C5' D:C2E501 4.5 33.0 1.0
C D:ASP158 4.6 23.8 1.0
CA D:ASP158 4.7 26.2 1.0
O3A D:C2E501 4.7 36.9 1.0
OE2 D:GLU128 4.9 25.4 1.0
O D:HOH613 5.0 42.2 1.0

Reference:

M.Yadav, K.Pal, U.Sen. Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Gmp Bound Form To Be Published.
Page generated: Wed Jul 9 14:51:35 2025

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