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Calcium in PDB 8j8t: Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1

Protein crystallography data

The structure of Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1, PDB code: 8j8t was solved by C.Zhang, P.Lu, K.Nagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.90 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.197, 47.305, 69.833, 90, 101.85, 90
R / Rfree (%) 16.6 / 23.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1 (pdb code 8j8t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1, PDB code: 8j8t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8j8t

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Calcium binding site 1 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:17.9
occ:1.00
 OD2 A:ASP75 2.3 15.5 1.0
OD2 A:ASP37 2.4 13.7 1.0
OD1 A:ASN98 2.4 20.3 1.0
O A:HOH311 2.4 18.7 1.0
OD1 A:ASP76 2.5 17.2 1.0
OD1 A:ASP75 2.7 17.0 1.0
CG A:ASP75 2.8 15.8 1.0
CG A:ASP37 3.3 13.7 1.0
CG A:ASP76 3.4 18.9 1.0
CG A:ASN98 3.4 22.0 1.0
CB A:ASP37 3.5 14.0 1.0
OD2 A:ASP76 3.7 21.9 1.0
ND2 A:ASN98 3.9 21.2 1.0
SG A:CYS99 4.0 19.5 1.0
ND2 A:ASN92 4.3 34.6 1.0
CB A:ASP75 4.3 15.6 1.0
N A:ASN98 4.4 16.4 1.0
OD1 A:ASP37 4.5 14.5 1.0
N A:ASP76 4.5 14.7 1.0
CB A:ASN98 4.7 19.6 1.0
CB A:ASP76 4.7 17.6 1.0
SG A:CYS35 4.9 18.0 1.0
CA A:ASN98 4.9 18.2 1.0
CE2 A:TYR38 5.0 26.1 1.0

Calcium binding site 2 out of 6 in 8j8t

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Calcium binding site 2 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:17.5
occ:1.00
 O A:TYR38 2.3 16.8 1.0
O A:VAL77 2.3 14.2 1.0
OD2 A:ASP40 2.4 16.3 1.0
OD2 A:ASP43 2.4 13.2 1.0
O A:HOH325 2.5 21.7 1.0
O A:HOH394 2.5 21.1 1.0
OD1 A:ASP43 2.7 14.1 1.0
CG A:ASP43 2.9 13.7 1.0
CG A:ASP40 3.2 16.8 1.0
C A:VAL77 3.4 15.5 1.0
C A:TYR38 3.5 16.9 1.0
OD1 A:ASP40 3.6 17.6 1.0
CA A:ARG78 3.9 18.7 1.0
N A:ARG78 4.1 17.1 1.0
O A:HOH346 4.1 36.7 1.0
N A:ASP40 4.2 15.6 1.0
O A:HOH364 4.2 30.1 1.0
N A:CYS79 4.2 15.6 1.0
CA A:TRP39 4.2 15.2 1.0
N A:TRP39 4.3 15.1 1.0
CB A:ASP40 4.4 16.0 1.0
CB A:ASP43 4.4 15.0 1.0
CB A:TYR38 4.4 20.3 1.0
C A:ARG78 4.5 18.7 1.0
CA A:TYR38 4.5 17.6 1.0
O A:HOH419 4.5 37.3 1.0
C A:TRP39 4.6 16.0 1.0
CA A:VAL77 4.7 16.1 1.0
O A:CYS79 4.8 17.7 1.0
CA A:ASP40 4.9 16.2 1.0
CB A:VAL77 5.0 15.5 1.0
N A:ASP43 5.0 14.9 1.0
N A:VAL77 5.0 16.2 1.0

Calcium binding site 3 out of 6 in 8j8t

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Calcium binding site 3 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:17.3
occ:1.00
 OE1 A:GLU103 2.2 16.9 1.0
OD1 A:ASP37 2.3 14.5 1.0
OD1 A:ASP36 2.3 14.7 1.0
O A:HOH328 2.4 18.4 1.0
CD A:GLU103 3.3 17.0 1.0
CG A:ASP36 3.3 15.3 1.0
CG A:ASP37 3.5 13.7 1.0
CG A:GLU103 3.7 16.4 1.0
OD2 A:ASP36 3.8 16.9 1.0
N A:ASP37 4.0 15.6 1.0
CA A:ASP37 4.2 14.7 1.0
C A:ASP36 4.2 16.3 1.0
CB A:GLU103 4.2 15.4 1.0
OD2 A:ASP37 4.4 13.7 1.0
OE2 A:GLU103 4.4 16.9 1.0
CB A:ASP37 4.4 14.0 1.0
SG A:CYS35 4.6 18.0 1.0
O A:ASP36 4.6 16.3 1.0
CB A:ASP36 4.6 16.0 1.0
O A:HOH306 4.8 30.4 1.0
CA A:ASP36 4.8 15.1 1.0
N A:ASP36 4.9 14.3 1.0

Calcium binding site 4 out of 6 in 8j8t

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Calcium binding site 4 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:25.5
occ:1.00
 OE1 B:GLU103 2.2 26.8 1.0
O B:HOH383 2.3 33.1 1.0
OD1 B:ASP36 2.3 24.6 1.0
OD1 B:ASP37 2.3 21.4 1.0
O B:HOH319 2.4 23.6 1.0
CD B:GLU103 3.3 23.3 1.0
CG B:ASP36 3.4 21.6 1.0
CG B:ASP37 3.6 21.4 1.0
CG B:GLU103 3.7 21.0 1.0
OD2 B:ASP36 3.8 21.4 1.0
N B:ASP37 4.0 21.6 1.0
CA B:ASP37 4.2 22.0 1.0
CB B:GLU103 4.2 22.1 1.0
C B:ASP36 4.3 21.4 1.0
OD2 B:ASP37 4.4 23.6 1.0
OE2 B:GLU103 4.4 24.2 1.0
CB B:ASP37 4.4 20.4 1.0
SG B:CYS35 4.5 22.4 1.0
CB B:ASP36 4.6 21.7 1.0
O B:ASP36 4.7 21.2 1.0
CA B:ASP36 4.9 22.7 1.0
O B:HOH345 4.9 32.3 1.0
N B:ASP36 4.9 21.8 1.0

Calcium binding site 5 out of 6 in 8j8t

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Calcium binding site 5 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:26.4
occ:1.00
 OD1 B:ASP76 2.2 29.4 1.0
OD2 B:ASP37 2.2 23.6 1.0
OD2 B:ASP75 2.3 22.9 1.0
OD1 B:ASN98 2.3 26.4 1.0
O B:HOH374 2.6 24.8 1.0
OD1 B:ASP75 2.7 20.6 1.0
CG B:ASP75 2.8 21.3 1.0
CG B:ASP37 3.2 21.4 1.0
CG B:ASP76 3.3 32.7 1.0
CG B:ASN98 3.4 26.1 1.0
CB B:ASP37 3.5 20.4 1.0
OD2 B:ASP76 3.7 35.3 1.0
ND2 B:ASN98 3.8 29.4 1.0
SG B:CYS99 3.9 24.7 1.0
ND2 B:ASN92 4.2 31.7 1.0
CB B:ASP75 4.3 21.2 1.0
OD1 B:ASP37 4.4 21.4 1.0
N B:ASP76 4.4 24.6 1.0
N B:ASN98 4.4 21.7 1.0
O B:HOH343 4.4 29.4 1.0
CB B:ASP76 4.5 29.2 1.0
CB B:ASN98 4.7 25.3 1.0
CA B:ASP76 4.8 27.4 1.0
SG B:CYS35 4.8 22.4 1.0
CA B:ASN98 4.9 26.1 1.0
CA B:ASP37 5.0 22.0 1.0

Calcium binding site 6 out of 6 in 8j8t

Go back to Calcium Binding Sites List in 8j8t
Calcium binding site 6 out of 6 in the Crystal Structure of Calcium-Saturated Srcr Domain 11 of DMBT1


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 Calcium-Saturated Srcr Domain 11 of DMBT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:23.5
occ:1.00
 OD2 B:ASP43 2.3 22.5 1.0
O B:TYR38 2.3 21.9 1.0
O B:VAL77 2.3 25.2 1.0
OD2 B:ASP40 2.4 27.4 1.0
O B:HOH321 2.4 25.4 1.0
O B:HOH382 2.6 25.9 1.0
OD1 B:ASP43 2.6 22.9 1.0
CG B:ASP43 2.8 22.8 1.0
CG B:ASP40 3.2 23.8 1.0
C B:VAL77 3.5 26.7 1.0
OD1 B:ASP40 3.5 27.8 1.0
C B:TYR38 3.5 22.4 1.0
CA B:ARG78 3.8 30.2 1.0
N B:ASP40 4.0 19.9 1.0
N B:ARG78 4.1 29.2 1.0
O B:HOH335 4.2 34.1 1.0
N B:CYS79 4.2 23.6 1.0
CA B:TRP39 4.2 20.9 1.0
CB B:ASP43 4.3 23.6 1.0
N B:TRP39 4.3 20.3 1.0
CB B:ASP40 4.4 25.0 1.0
C B:ARG78 4.5 28.5 1.0
C B:TRP39 4.5 21.5 1.0
CB B:TYR38 4.5 25.8 1.0
CA B:TYR38 4.6 22.4 1.0
CA B:VAL77 4.7 26.1 1.0
O B:CYS79 4.8 26.4 1.0
N B:ASP43 4.8 24.2 1.0
CA B:ASP40 4.8 23.2 1.0
CB B:ARG78 4.8 34.0 1.0
CG B:ARG78 4.9 37.2 1.0
CB B:VAL77 5.0 25.4 1.0

Reference:

C.Zhang, P.Lu, K.Nagata. Crystal Structure of Calcium-Saturated Srcr Domain 11 of Salsa To Be Published.
Page generated: Thu Jul 10 05:27:14 2025

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