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Calcium in PDB 3s3t: Universal Stress Protein Uspa From Lactobacillus Plantarum

Protein crystallography data

The structure of Universal Stress Protein Uspa From Lactobacillus Plantarum, PDB code: 3s3t was solved by J.Osipiuk, H.Li, G.Cobb, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.50 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.015, 56.187, 109.144, 102.13, 100.53, 90.36
R / Rfree (%) 16.8 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Universal Stress Protein Uspa From Lactobacillus Plantarum (pdb code 3s3t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Universal Stress Protein Uspa From Lactobacillus Plantarum, PDB code: 3s3t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3s3t

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Calcium binding site 1 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:26.6
occ:1.00
 O2B A:ATP501 2.1 21.9 1.0
O1A A:ATP501 2.2 18.2 1.0
O A:HOH246 2.2 28.9 1.0
O A:HOH157 2.4 24.2 1.0
O1G A:ATP501 2.4 21.3 1.0
O A:HOH148 2.5 36.5 1.0
PB A:ATP501 3.3 21.1 1.0
PA A:ATP501 3.4 18.0 1.0
PG A:ATP501 3.7 23.6 1.0
O3A A:ATP501 3.7 22.4 1.0
O3B A:ATP501 3.8 19.3 1.0
OG1 A:THR130 4.1 19.2 1.0
O5' A:ATP501 4.3 17.2 1.0
N7 A:ATP501 4.4 17.1 1.0
C8 A:ATP501 4.5 19.4 1.0
O2G A:ATP501 4.5 23.3 1.0
O2A A:ATP501 4.5 16.5 1.0
OG1 A:THR119 4.6 24.6 1.0
N A:ASN120 4.6 24.8 1.0
CB A:ASN120 4.6 25.6 1.0
N A:THR119 4.6 21.8 1.0
O1B A:ATP501 4.6 18.8 1.0
OD2 A:ASP13 4.7 23.8 1.0
CG A:ASN120 4.8 28.9 1.0
O A:HOH284 4.8 33.0 1.0
O3G A:ATP501 4.8 24.2 1.0
ND2 A:ASN120 4.9 28.4 1.0

Calcium binding site 2 out of 8 in 3s3t

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Calcium binding site 2 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:27.5
occ:1.00
 O2B B:ATP501 2.2 22.2 1.0
O B:HOH309 2.3 34.2 1.0
O1A B:ATP501 2.3 18.2 1.0
O B:HOH303 2.3 26.1 1.0
O B:HOH586 2.3 41.8 1.0
O3G B:ATP501 2.3 20.5 1.0
PB B:ATP501 3.3 20.1 1.0
PA B:ATP501 3.5 19.1 1.0
PG B:ATP501 3.6 20.4 1.0
O3B B:ATP501 3.8 19.1 1.0
O3A B:ATP501 3.8 21.4 1.0
OG1 B:THR130 4.1 20.2 1.0
OG1 B:THR119 4.3 29.2 1.0
O B:HOH531 4.4 32.1 1.0
O5' B:ATP501 4.4 21.1 1.0
CB B:ASN120 4.4 21.1 1.0
N7 B:ATP501 4.5 22.4 1.0
O1G B:ATP501 4.5 20.9 1.0
O B:HOH791 4.5 40.7 1.0
N B:ASN120 4.6 21.1 1.0
C8 B:ATP501 4.6 19.8 1.0
O B:HOH366 4.6 36.7 1.0
O1B B:ATP501 4.7 18.3 1.0
O2A B:ATP501 4.7 15.2 1.0
O B:HOH154 4.7 42.9 1.0
O2G B:ATP501 4.7 22.6 1.0
N B:THR119 4.7 21.0 1.0
OD2 B:ASP13 4.7 26.9 1.0
CG B:ASN120 4.8 26.9 1.0
ND2 B:ASN120 4.9 26.3 1.0
O B:HOH264 4.9 29.0 1.0

Calcium binding site 3 out of 8 in 3s3t

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Calcium binding site 3 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:24.8
occ:1.00
 O C:HOH340 2.2 26.0 1.0
O1B C:ATP501 2.2 19.6 1.0
O2A C:ATP501 2.2 17.9 1.0
O1G C:ATP501 2.4 21.8 1.0
O C:HOH159 2.4 21.3 1.0
O C:HOH156 2.5 28.9 1.0
PB C:ATP501 3.3 17.9 1.0
PA C:ATP501 3.5 15.0 1.0
PG C:ATP501 3.6 22.2 1.0
O3A C:ATP501 3.7 18.9 1.0
O3B C:ATP501 3.8 18.6 1.0
OG1 C:THR130 4.2 17.8 1.0
O C:HOH746 4.2 31.0 1.0
CB C:ASN120 4.3 26.2 1.0
O5' C:ATP501 4.3 15.3 1.0
N7 C:ATP501 4.3 15.0 1.0
O2G C:ATP501 4.5 21.0 1.0
O C:HOH747 4.5 26.3 1.0
C8 C:ATP501 4.5 17.7 1.0
O2B C:ATP501 4.5 16.9 1.0
N C:ASN120 4.6 23.2 1.0
OG1 C:THR119 4.6 26.7 1.0
O1A C:ATP501 4.6 12.6 1.0
N C:THR119 4.6 21.1 1.0
CG C:ASN120 4.6 30.5 1.0
O3G C:ATP501 4.7 21.1 1.0
OD2 C:ASP13 4.7 19.9 1.0
O C:HOH212 4.8 27.8 1.0
OD1 C:ASN120 4.8 35.4 1.0
O C:HOH307 5.0 38.2 1.0
O C:HOH748 5.0 33.6 1.0

Calcium binding site 4 out of 8 in 3s3t

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Calcium binding site 4 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:23.8
occ:1.00
 O2B D:ATP501 2.1 21.9 1.0
O2A D:ATP501 2.2 17.7 1.0
O D:HOH675 2.2 21.4 1.0
O1G D:ATP501 2.2 25.5 1.0
O D:HOH819 2.3 41.4 1.0
O D:HOH673 2.5 23.6 1.0
O D:HOH674 2.5 25.8 1.0
PB D:ATP501 3.3 20.7 1.0
PA D:ATP501 3.4 17.1 1.0
PG D:ATP501 3.5 22.0 1.0
O3A D:ATP501 3.7 18.0 1.0
O3B D:ATP501 3.8 20.0 1.0
OG1 D:THR130 4.2 18.8 1.0
O5' D:ATP501 4.3 14.8 1.0
O D:HOH295 4.3 29.4 1.0
N7 D:ATP501 4.4 15.3 1.0
CB D:ASN120 4.4 27.7 1.0
O3G D:ATP501 4.4 24.7 1.0
OG1 D:THR119 4.5 23.1 1.0
O D:HOH741 4.5 34.9 1.0
C8 D:ATP501 4.5 15.3 1.0
O1B D:ATP501 4.6 20.5 1.0
OD2 D:ASP13 4.6 17.6 1.0
O2G D:ATP501 4.6 23.9 1.0
O1A D:ATP501 4.6 15.8 1.0
CG D:ASN120 4.7 32.6 1.0
N D:THR119 4.7 21.0 1.0
N D:ASN120 4.7 23.9 1.0
O D:HOH740 4.8 37.2 1.0
OD1 D:ASN120 4.9 37.1 1.0

Calcium binding site 5 out of 8 in 3s3t

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Calcium binding site 5 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:27.7
occ:1.00
 O2B E:ATP501 2.1 19.8 1.0
O1A E:ATP501 2.2 21.0 1.0
O E:HOH220 2.3 31.2 1.0
O E:HOH283 2.4 26.6 1.0
O3G E:ATP501 2.4 25.4 1.0
O E:HOH420 2.5 28.1 1.0
PB E:ATP501 3.2 20.6 1.0
PA E:ATP501 3.4 20.9 1.0
PG E:ATP501 3.6 24.4 1.0
O3A E:ATP501 3.6 24.0 1.0
O3B E:ATP501 3.7 22.0 1.0
OG1 E:THR130 4.1 20.5 1.0
O5' E:ATP501 4.3 19.5 1.0
N7 E:ATP501 4.4 23.6 1.0
O E:HOH590 4.5 32.8 1.0
O2G E:ATP501 4.5 24.4 1.0
OG1 E:THR119 4.5 26.9 1.0
N E:THR119 4.5 23.5 1.0
O2A E:ATP501 4.6 22.5 1.0
C8 E:ATP501 4.6 20.0 1.0
OD2 E:ASP13 4.6 22.8 1.0
N E:ASN120 4.6 26.1 1.0
O E:HOH424 4.6 27.9 1.0
CB E:ASN120 4.6 26.6 1.0
O1B E:ATP501 4.7 20.9 1.0
O1G E:ATP501 4.8 24.2 1.0
O E:HOH796 4.9 33.8 1.0
CG E:ASN120 4.9 28.7 1.0

Calcium binding site 6 out of 8 in 3s3t

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Calcium binding site 6 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:28.1
occ:1.00
 O2A F:ATP501 2.1 24.5 1.0
O2B F:ATP501 2.1 20.1 1.0
O F:HOH446 2.2 37.9 1.0
O F:HOH155 2.3 25.6 1.0
O F:HOH495 2.3 27.8 1.0
O2G F:ATP501 2.4 24.1 1.0
PB F:ATP501 3.3 21.5 1.0
PA F:ATP501 3.5 19.9 1.0
PG F:ATP501 3.6 25.9 1.0
O3B F:ATP501 3.8 24.0 1.0
O3A F:ATP501 3.9 20.3 1.0
OG1 F:THR130 4.2 25.8 1.0
O5' F:ATP501 4.3 20.6 1.0
N7 F:ATP501 4.4 26.8 1.0
O3G F:ATP501 4.4 22.9 1.0
OG1 F:THR119 4.4 29.9 1.0
CB F:ASN120 4.5 25.8 1.0
C8 F:ATP501 4.5 26.6 1.0
N F:ASN120 4.6 25.6 1.0
CG F:ASN120 4.6 31.3 1.0
OD2 F:ASP13 4.6 28.6 1.0
O1A F:ATP501 4.6 17.6 1.0
O1B F:ATP501 4.7 21.1 1.0
N F:THR119 4.7 24.2 1.0
O1G F:ATP501 4.8 25.8 1.0
ND2 F:ASN120 4.9 33.0 1.0
OD1 F:ASN120 5.0 32.9 1.0

Calcium binding site 7 out of 8 in 3s3t

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Calcium binding site 7 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca502

b:23.8
occ:1.00
 O1B G:ATP501 2.2 18.4 1.0
O G:HOH787 2.2 27.8 1.0
O2G G:ATP501 2.2 20.7 1.0
O2A G:ATP501 2.3 15.7 1.0
O G:HOH166 2.5 23.1 1.0
O G:HOH466 2.5 43.1 1.0
PB G:ATP501 3.3 19.4 1.0
PA G:ATP501 3.5 16.4 1.0
PG G:ATP501 3.6 23.9 1.0
O3A G:ATP501 3.7 19.4 1.0
O3B G:ATP501 3.8 19.7 1.0
OG1 G:THR130 4.0 19.9 1.0
O5' G:ATP501 4.4 16.7 1.0
N7 G:ATP501 4.4 17.9 1.0
OG1 G:THR119 4.5 25.8 1.0
O1G G:ATP501 4.5 21.7 1.0
O G:HOH387 4.5 31.1 1.0
C8 G:ATP501 4.5 20.4 1.0
O3G G:ATP501 4.6 20.3 1.0
O1A G:ATP501 4.6 17.0 1.0
CB G:ASN120 4.6 26.9 1.0
N G:ASN120 4.6 25.6 1.0
O2B G:ATP501 4.7 19.0 1.0
O G:HOH882 4.7 38.0 1.0
N G:THR119 4.7 23.6 1.0
O G:HOH265 4.8 35.0 1.0
OD2 G:ASP13 4.8 20.9 1.0
CG G:ASN120 4.8 29.4 1.0

Calcium binding site 8 out of 8 in 3s3t

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Calcium binding site 8 out of 8 in the Universal Stress Protein Uspa From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Universal Stress Protein Uspa From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca502

b:27.4
occ:1.00
 O H:HOH291 2.2 25.6 1.0
O1B H:ATP501 2.2 27.8 1.0
O2A H:ATP501 2.3 21.8 1.0
O H:HOH270 2.4 25.3 1.0
O H:HOH768 2.4 33.7 1.0
O3G H:ATP501 2.5 28.8 1.0
PB H:ATP501 3.3 25.4 1.0
PA H:ATP501 3.5 20.1 1.0
PG H:ATP501 3.7 28.0 1.0
O3A H:ATP501 3.7 20.8 1.0
O3B H:ATP501 3.9 26.9 1.0
OG1 H:THR130 4.1 19.8 1.0
O H:HOH561 4.3 28.1 1.0
O5' H:ATP501 4.3 18.8 1.0
N7 H:ATP501 4.3 21.7 1.0
OG1 H:THR119 4.4 31.0 1.0
CB H:ASN120 4.4 33.2 1.0
O H:HOH687 4.5 28.1 1.0
C8 H:ATP501 4.5 22.5 1.0
O2G H:ATP501 4.5 28.3 1.0
N H:ASN120 4.6 30.3 1.0
OD2 H:ASP13 4.7 19.6 1.0
O1A H:ATP501 4.7 20.4 1.0
O2B H:ATP501 4.7 23.7 1.0
N H:THR119 4.7 28.1 1.0
CG H:ASN120 4.8 37.7 1.0
O H:HOH425 4.8 36.5 1.0
O1G H:ATP501 4.9 31.0 1.0
O H:HOH334 4.9 33.8 1.0

Reference:

J.Osipiuk, H.Li, G.Cobb, A.Joachimiak. Universal Stress Protein Uspa From Lactobacillus Plantarum. To Be Published.
Page generated: Sat Jul 13 19:01:43 2024

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