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Calcium in PDB 6k6t: Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Imp Bound Form

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

All present enzymatic activity of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Imp Bound Form:
3.1.4.1;

Protein crystallography data

The structure of Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Imp Bound Form, PDB code: 6k6t 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) 51.11 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.450, 42.540, 155.040, 90.00, 94.65, 90.00
R / Rfree (%) 19.7 / 25.2

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-Imp Bound Form (pdb code 6k6t). 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-Imp Bound Form, PDB code: 6k6t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:24.4
occ:1.00
 OE2 A:GLU128 2.2 22.4 1.0
OD2 A:ASP158 2.4 25.2 1.0
OD1 A:ASN95 2.4 24.3 1.0
OE2 A:GLU45 2.4 33.7 1.0
O A:HOH601 2.4 22.8 1.0
O2P A:C2I501 2.4 31.3 1.0
CG A:ASP158 3.1 22.7 1.0
CG A:ASN95 3.3 33.4 1.0
CD A:GLU45 3.3 31.4 1.0
CD A:GLU128 3.4 25.8 1.0
OD1 A:ASP158 3.4 26.2 1.0
ND2 A:ASN95 3.5 24.8 1.0
P1 A:C2I501 3.6 28.5 1.0
OE1 A:GLU45 3.8 28.7 1.0
O5' A:C2I501 3.8 31.5 1.0
O A:HOH620 3.9 29.0 1.0
O1P A:C2I501 3.9 28.1 1.0
CA A:CA503 4.0 51.2 1.0
NZ A:LYS179 4.0 21.5 1.0
OE1 A:GLU128 4.1 21.7 1.0
O2A A:C2I501 4.1 36.7 1.0
CB A:GLU128 4.3 32.4 1.0
CB A:ASP158 4.3 22.4 1.0
CG A:GLU128 4.4 27.6 1.0
OE2 A:GLU215 4.4 35.5 1.0
CG A:GLU45 4.5 23.1 1.0
CB A:ASN95 4.7 30.9 1.0

Calcium binding site 2 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:51.2
occ:1.00
 OE1 A:GLU215 2.3 30.7 1.0
OD1 A:ASP159 2.3 35.2 1.0
O1P A:C2I501 2.3 28.1 1.0
OD1 A:ASP158 2.5 26.2 1.0
CD A:GLU215 3.0 31.9 1.0
CG A:ASP158 3.1 22.7 1.0
OD2 A:ASP158 3.2 25.2 1.0
O A:HOH601 3.2 22.8 1.0
OE2 A:GLU215 3.3 35.5 1.0
CG A:ASP159 3.3 36.6 1.0
P1 A:C2I501 3.6 28.5 1.0
O A:HOH649 3.6 24.7 1.0
N A:ASP159 3.7 22.0 1.0
O A:HOH620 3.7 29.0 1.0
O2P A:C2I501 3.9 31.3 1.0
OD2 A:ASP159 4.0 43.2 1.0
CA A:CA502 4.0 24.4 1.0
O A:HOH680 4.0 30.2 1.0
CA A:ASP159 4.1 25.5 1.0
O5' A:C2I501 4.1 31.5 1.0
CB A:ASP159 4.3 28.7 1.0
CG A:GLU215 4.4 31.4 1.0
CB A:ASP158 4.4 22.4 1.0
O A:HOH670 4.4 43.3 1.0
C A:ASP158 4.7 25.0 1.0
O A:HOH642 4.8 34.4 1.0
CA A:ASP158 4.8 24.5 1.0
OD1 A:ASP181 4.9 30.5 1.0
O3A A:C2I501 5.0 26.9 1.0

Calcium binding site 3 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:21.8
occ:1.00
 OE2 B:GLU128 2.2 23.5 1.0
O1P B:C2I501 2.3 32.6 1.0
OD2 B:ASP158 2.4 28.6 1.0
OE2 B:GLU45 2.4 27.4 1.0
O B:HOH601 2.4 21.5 1.0
OD1 B:ASN95 2.4 24.8 1.0
CG B:ASP158 3.2 24.7 1.0
CD B:GLU45 3.4 24.8 1.0
CD B:GLU128 3.4 22.4 1.0
CG B:ASN95 3.4 23.8 1.0
OD1 B:ASP158 3.5 24.7 1.0
P1 B:C2I501 3.6 30.9 1.0
ND2 B:ASN95 3.7 24.1 1.0
CA B:CA503 3.7 94.8 1.0
OE1 B:GLU45 3.8 26.2 1.0
O5' B:C2I501 4.0 36.1 1.0
OE1 B:GLU128 4.1 20.5 1.0
O2P B:C2I501 4.1 40.8 1.0
O B:HOH635 4.2 25.1 1.0
CB B:GLU128 4.2 24.3 1.0
O2A B:C2I501 4.3 40.2 1.0
CG B:GLU128 4.4 22.3 1.0
NZ B:LYS179 4.4 20.6 1.0
CB B:ASP158 4.4 25.9 1.0
CG B:GLU45 4.5 24.9 1.0
OE2 B:GLU215 4.5 47.1 1.0
CB B:ASN95 4.7 23.7 1.0
O3A B:C2I501 5.0 31.9 1.0

Calcium binding site 4 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:94.8
occ:1.00
 OD1 B:ASP159 2.3 36.3 1.0
OE1 B:GLU215 2.3 42.2 1.0
OD1 B:ASP158 2.5 24.7 1.0
O2P B:C2I501 2.5 40.8 1.0
O B:HOH601 2.9 21.5 1.0
CD B:GLU215 3.0 42.3 1.0
CG B:ASP158 3.0 24.7 1.0
OD2 B:ASP158 3.1 28.6 1.0
OE2 B:GLU215 3.1 47.1 1.0
CG B:ASP159 3.2 34.6 1.0
O1P B:C2I501 3.4 32.6 1.0
P1 B:C2I501 3.6 30.9 1.0
OD2 B:ASP159 3.6 36.4 1.0
CA B:CA502 3.7 21.8 1.0
O B:HOH653 3.8 22.6 1.0
N B:ASP159 3.9 22.4 1.0
O5' B:C2I501 4.0 36.1 1.0
O B:HOH635 4.0 25.1 1.0
CA B:ASP159 4.3 30.8 1.0
CB B:ASP159 4.3 31.7 1.0
CB B:ASP158 4.3 25.9 1.0
CG B:GLU215 4.4 36.6 1.0
C B:ASP158 4.7 22.5 1.0
OE2 B:GLU128 4.8 23.5 1.0
CA B:ASP158 4.8 22.1 1.0
O3A B:C2I501 4.8 31.9 1.0

Calcium binding site 5 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:26.1
occ:1.00
 O2P C:C2I501 2.1 28.6 1.0
OE2 C:GLU128 2.2 24.5 1.0
ND2 C:ASN95 2.2 24.1 1.0
O C:HOH601 2.2 21.1 1.0
OD2 C:ASP158 2.3 28.9 1.0
OE2 C:GLU45 2.5 22.1 1.0
CG C:ASP158 3.1 26.2 1.0
CG C:ASN95 3.3 26.1 1.0
CD C:GLU45 3.3 25.7 1.0
CD C:GLU128 3.4 26.2 1.0
OD1 C:ASP158 3.5 29.1 1.0
P1 C:C2I501 3.6 28.9 1.0
OD1 C:ASN95 3.6 25.3 1.0
OE1 C:GLU45 3.8 22.1 1.0
O C:HOH628 3.9 38.8 1.0
CA C:CA503 3.9 54.6 1.0
O C:HOH644 4.0 37.2 1.0
O5' C:C2I501 4.1 30.7 1.0
NZ C:LYS179 4.1 20.1 1.0
O1P C:C2I501 4.1 27.6 1.0
OE1 C:GLU128 4.2 23.3 1.0
CB C:GLU128 4.2 24.2 1.0
CB C:ASP158 4.2 23.9 1.0
OE1 C:GLU215 4.3 37.9 1.0
CG C:GLU128 4.4 25.7 1.0
O3A C:C2I501 4.4 40.1 1.0
O2A C:C2I501 4.5 50.7 1.0
CG C:GLU45 4.5 25.6 1.0
CB C:ASN95 4.6 27.2 1.0
CD C:LYS179 4.9 19.5 1.0

Calcium binding site 6 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:54.6
occ:1.00
 OE2 C:GLU215 2.2 35.3 1.0
O1P C:C2I501 2.5 27.6 1.0
OD1 C:ASP159 2.6 35.7 1.0
OD1 C:ASP158 2.6 29.1 1.0
OE1 C:GLU215 2.8 37.9 1.0
CD C:GLU215 2.9 34.5 1.0
O C:HOH601 2.9 21.1 1.0
CG C:ASP158 3.3 26.2 1.0
P1 C:C2I501 3.3 28.9 1.0
OD2 C:ASP158 3.3 28.9 1.0
O C:HOH602 3.3 39.0 1.0
O2P C:C2I501 3.4 28.6 1.0
O5' C:C2I501 3.5 30.7 1.0
CG C:ASP159 3.6 32.3 1.0
CA C:CA502 3.9 26.1 1.0
O C:HOH640 4.1 38.9 1.0
N C:ASP159 4.1 23.8 1.0
OD2 C:ASP159 4.1 37.9 1.0
O C:HOH628 4.2 38.8 1.0
CG C:GLU215 4.4 33.5 1.0
CA C:ASP159 4.5 24.0 1.0
CB C:ASP159 4.6 25.4 1.0
CB C:ASP158 4.7 23.9 1.0
O3A C:C2I501 4.9 40.1 1.0
C5' C:C2I501 4.9 30.0 1.0
C C:ASP158 5.0 23.1 1.0

Calcium binding site 7 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:27.6
occ:1.00
 OE2 D:GLU128 2.2 30.4 1.0
O D:HOH604 2.2 26.1 1.0
ND2 D:ASN95 2.2 27.0 1.0
OE2 D:GLU45 2.3 31.5 1.0
OD2 D:ASP158 2.4 29.3 1.0
O2P D:C2I501 2.5 28.2 1.0
CG D:ASP158 3.3 28.5 1.0
CD D:GLU128 3.3 32.1 1.0
CD D:GLU45 3.3 30.1 1.0
CG D:ASN95 3.3 35.4 1.0
CA D:CA503 3.7 65.9 1.0
OD1 D:ASN95 3.7 36.6 1.0
OD1 D:ASP158 3.7 23.7 1.0
P1 D:C2I501 3.8 31.2 1.0
OE1 D:GLU45 3.8 25.0 1.0
O1P D:C2I501 3.9 32.1 1.0
OE1 D:GLU128 3.9 31.8 1.0
O2A D:C2I501 4.0 54.1 1.0
NZ D:LYS179 4.2 23.5 1.0
O5' D:C2I501 4.2 37.0 1.0
CB D:GLU128 4.2 29.1 1.0
CG D:GLU128 4.3 31.7 1.0
CB D:ASP158 4.4 24.3 1.0
CG D:GLU45 4.5 25.8 1.0
OE2 D:GLU215 4.5 46.8 1.0
CB D:ASN95 4.6 32.5 1.0
CD D:LYS179 4.9 22.8 1.0

Calcium binding site 8 out of 8 in 6k6t

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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-Imp 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-Imp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:65.9
occ:1.00
 O1P D:C2I501 2.3 32.1 1.0
OE1 D:GLU215 2.4 39.5 1.0
OD1 D:ASP158 2.4 23.7 1.0
OD1 D:ASP159 2.4 42.4 1.0
OD2 D:ASP158 2.7 29.3 1.0
O D:HOH604 2.8 26.1 1.0
CG D:ASP158 2.8 28.5 1.0
CD D:GLU215 3.1 43.7 1.0
CG D:ASP159 3.2 41.4 1.0
OE2 D:GLU215 3.2 46.8 1.0
P1 D:C2I501 3.5 31.2 1.0
OD2 D:ASP159 3.6 45.2 1.0
CA D:CA502 3.7 27.6 1.0
O2P D:C2I501 3.7 28.2 1.0
N D:ASP159 3.9 30.5 1.0
O D:HOH644 4.0 40.3 1.0
O5' D:C2I501 4.0 37.0 1.0
CB D:ASP158 4.2 24.3 1.0
CA D:ASP159 4.3 32.5 1.0
CB D:ASP159 4.3 37.9 1.0
CG D:GLU215 4.5 43.9 1.0
C D:ASP158 4.7 29.1 1.0
OE2 D:GLU128 4.8 30.4 1.0
CA D:ASP158 4.8 25.2 1.0
O3A D:C2I501 4.8 36.9 1.0

Reference:

M.Yadav, K.Pal, U.Sen. Crystal Structure of A Standalone Versatile Eal Protein From Vibrio Cholerae O395 - C-Di-Imp Bound Form To Be Published.
Page generated: Wed Jul 9 15:24:25 2025

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