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Calcium in PDB 4eqb: 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes

Protein crystallography data

The structure of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes, PDB code: 4eqb was solved by G.Minasov, Z.Wawrzak, P.J.Stogios, M.Kudritska, V.Yim, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.635, 54.347, 76.704, 75.83, 80.87, 77.56
R / Rfree (%) 15.5 / 18.6

Other elements in 4eqb:

The structure of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes (pdb code 4eqb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes, PDB code: 4eqb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4eqb

Go back to Calcium Binding Sites List in 4eqb
Calcium binding site 1 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:15.4
occ:1.00
 O A:HOH527 2.2 16.5 1.0
OE1 A:GLN53 2.3 13.6 1.0
OD1 A:ASN289 2.4 11.2 1.0
O A:HOH517 2.5 13.0 1.0
CD A:GLN53 3.4 13.0 1.0
CG A:ASN289 3.6 10.7 1.0
NE2 A:GLN53 4.0 16.4 1.0
ND2 A:ASN289 4.1 10.5 1.0
OE1 A:GLN292 4.5 13.7 1.0
CG A:GLN53 4.6 13.2 1.0
CD2 A:LEU50 4.6 13.4 1.0
OE2 A:GLU57 4.6 30.3 1.0
CB A:GLN53 4.8 12.2 1.0
OE1 A:GLU288 4.8 12.3 1.0
OE1 A:GLU57 4.8 23.6 1.0
CB A:ASN289 4.8 9.9 1.0
CZ A:PHE283 4.9 15.1 1.0
CB A:GLU288 4.9 12.5 1.0
CA A:ASN289 4.9 9.8 1.0
N A:ASN289 4.9 10.2 1.0

Calcium binding site 2 out of 8 in 4eqb

Go back to Calcium Binding Sites List in 4eqb
Calcium binding site 2 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.5
occ:1.00
 O A:TYR354 2.3 19.6 1.0
O A:HOH993 2.3 22.2 1.0
OXT A:LYS356 2.3 22.1 1.0
O A:HOH994 2.4 28.0 1.0
C A:TYR354 3.5 20.1 1.0
C A:LYS356 3.6 23.0 1.0
C A:ARG355 4.0 23.0 1.0
N A:LYS356 4.1 22.9 1.0
O A:ARG355 4.3 25.4 1.0
CA A:ARG355 4.3 21.0 1.0
N A:ARG355 4.4 20.4 1.0
O A:LYS356 4.4 26.1 1.0
CA A:TYR354 4.4 19.5 1.0
CA A:LYS356 4.5 24.6 1.0
CD1 A:TYR354 4.7 20.2 1.0
CG A:TYR354 4.8 20.0 1.0
O A:HOH576 5.0 22.9 1.0
CE1 A:TYR354 5.0 19.7 1.0
O A:MET353 5.0 22.7 0.6

Calcium binding site 3 out of 8 in 4eqb

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Calcium binding site 3 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:16.6
occ:0.60
 O A:HOH633 2.4 20.8 1.0
O A:HOH561 2.4 17.3 1.0
O B:HOH561 2.4 22.1 1.0
O A:THR66 2.4 13.2 1.0
OE1 B:GLN292 2.5 14.2 1.0
OG1 A:THR66 2.5 13.2 1.0
C A:THR66 3.1 12.5 1.0
CD B:GLN292 3.2 13.8 1.0
CB A:THR66 3.5 11.0 1.0
CA A:THR66 3.6 11.1 1.0
N A:THR66 3.8 13.0 1.0
NE2 B:GLN292 3.9 14.2 1.0
OE2 B:GLU49 4.0 19.6 1.0
CG B:GLN292 4.0 13.5 1.0
O A:HOH508 4.0 14.6 1.0
N A:PHE67 4.1 11.8 1.0
O A:HOH533 4.2 14.3 1.0
O A:HOH531 4.3 19.0 1.0
O B:HOH507 4.4 13.6 1.0
O A:HOH892 4.4 41.3 1.0
NE2 B:GLN53 4.5 16.1 1.0
O B:HOH667 4.5 35.8 1.0
CA A:PHE67 4.5 12.9 1.0
CB B:GLN292 4.6 12.1 1.0
OD2 A:ASP68 4.8 17.6 1.0
CG2 A:THR66 4.8 13.2 1.0
O B:HOH632 4.9 25.2 1.0
O B:HOH652 4.9 22.4 1.0
O B:HOH513 4.9 17.1 1.0

Calcium binding site 4 out of 8 in 4eqb

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Calcium binding site 4 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:12.5
occ:0.40
 O A:HOH945 2.2 33.6 1.0
O A:HOH906 2.4 31.5 1.0
O1S A:EPE406 2.4 20.9 0.7
O A:HOH588 2.4 24.7 1.0
O A:GLY43 2.4 13.4 1.0
O A:HOH785 2.5 30.1 1.0
O A:HOH680 2.5 25.2 1.0
C A:GLY43 3.5 12.5 1.0
S A:EPE406 3.7 21.4 0.7
CB A:ASP44 3.9 15.1 1.0
O A:HOH784 4.1 32.5 1.0
O3S A:EPE406 4.1 22.3 0.7
CA A:GLY43 4.3 12.1 1.0
O A:ASP44 4.3 14.0 1.0
N A:ASP44 4.3 12.4 1.0
C10 A:EPE406 4.4 17.6 0.7
O B:HOH743 4.4 34.9 1.0
O A:HOH701 4.4 28.9 1.0
CA A:ASP44 4.4 12.8 1.0
O A:HOH813 4.4 32.3 1.0
OD1 A:ASP68 4.5 22.6 1.0
C A:ASP44 4.5 12.3 1.0
N A:GLY43 4.5 11.5 1.0
O A:HOH637 4.5 25.3 1.0
OD2 A:ASP44 4.5 22.8 1.0
O B:HOH740 4.5 31.0 1.0
CG A:ASP44 4.8 21.7 1.0
O2S A:EPE406 4.8 24.2 0.7
OE2 B:GLU57 4.9 23.3 0.6
O B:HOH516 5.0 16.0 1.0

Calcium binding site 5 out of 8 in 4eqb

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Calcium binding site 5 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:12.5
occ:0.80
 O B:HOH579 2.2 17.1 1.0
OE1 B:GLN53 2.3 13.4 1.0
OD1 B:ASN289 2.4 12.9 1.0
O B:HOH507 2.4 13.6 1.0
O A:HOH508 2.5 14.6 1.0
O B:HOH516 2.5 16.0 1.0
O B:HOH521 2.6 19.4 1.0
CD B:GLN53 3.4 13.3 1.0
CG B:ASN289 3.6 12.1 1.0
NE2 B:GLN53 3.9 16.1 1.0
ND2 B:ASN289 4.1 12.8 1.0
OD2 A:ASP44 4.3 22.8 1.0
CG B:GLN53 4.5 13.1 1.0
O A:HOH754 4.5 29.2 1.0
CD2 B:LEU50 4.5 12.3 1.0
OE1 B:GLN292 4.5 14.2 1.0
OE2 B:GLU57 4.5 23.3 0.6
OD2 A:ASP68 4.6 17.6 1.0
CA A:GLY43 4.7 12.1 1.0
OG1 A:THR66 4.7 13.2 1.0
OE1 B:GLU288 4.7 13.6 1.0
CB B:GLU288 4.8 13.8 1.0
OE1 B:GLU57 4.8 16.9 0.6
OD1 A:ASP68 4.8 22.6 1.0
CB B:GLN53 4.8 11.5 1.0
CB B:ASN289 4.8 10.6 1.0
CZ B:PHE283 4.9 13.6 1.0
CA B:ASN289 4.9 11.0 1.0
N B:ASN289 4.9 11.0 1.0
O A:HOH680 5.0 25.2 1.0
C B:GLU288 5.0 12.1 1.0

Calcium binding site 6 out of 8 in 4eqb

Go back to Calcium Binding Sites List in 4eqb
Calcium binding site 6 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:17.4
occ:1.00
 O B:TYR354 2.2 19.4 0.3
O B:HOH901 2.3 26.9 1.0
O B:TYR354 2.3 17.4 0.7
OXT B:LYS356 2.3 21.1 1.0
O B:HOH902 2.4 24.2 1.0
C B:TYR354 3.4 19.6 0.3
C B:TYR354 3.4 19.7 0.7
C B:LYS356 3.6 22.1 1.0
C B:ARG355 4.0 23.4 1.0
N B:LYS356 4.1 23.1 1.0
O B:ARG355 4.3 24.6 1.0
CA B:TYR354 4.3 19.5 0.7
CA B:TYR354 4.3 18.3 0.3
N B:ARG355 4.4 20.4 1.0
O B:LYS356 4.4 23.4 1.0
CA B:ARG355 4.4 22.6 1.0
CA B:LYS356 4.5 25.2 1.0
CD1 B:TYR354 4.7 22.9 0.7
O B:MET353 4.8 20.4 0.5
CG B:TYR354 4.8 20.0 0.7
CB B:TYR354 4.9 17.7 0.3
CE1 B:TYR354 5.0 20.1 0.7

Calcium binding site 7 out of 8 in 4eqb

Go back to Calcium Binding Sites List in 4eqb
Calcium binding site 7 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:16.9
occ:0.60
 O B:HOH520 2.4 17.5 1.0
O B:HOH574 2.4 19.8 1.0
O B:THR66 2.4 13.3 1.0
OG1 B:THR66 2.5 12.6 1.0
C B:THR66 3.2 12.5 1.0
CB B:THR66 3.6 10.5 1.0
CA B:THR66 3.7 12.4 1.0
N B:THR66 3.8 12.7 1.0
O B:HOH506 4.1 15.7 1.0
N B:PHE67 4.1 11.9 1.0
O B:HOH542 4.2 20.1 1.0
O B:HOH510 4.2 12.6 1.0
CA B:PHE67 4.6 14.2 1.0
CG2 B:THR66 4.8 12.1 1.0
OD2 B:ASP68 4.8 18.9 1.0

Calcium binding site 8 out of 8 in 4eqb

Go back to Calcium Binding Sites List in 4eqb
Calcium binding site 8 out of 8 in the 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein Potd From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:22.6
occ:0.60
 O B:HOH874 2.3 34.5 1.0
O B:HOH597 2.4 25.6 1.0
O1S B:EPE406 2.4 27.4 0.7
O B:GLY43 2.4 14.6 1.0
O B:HOH678 2.5 27.2 1.0
O B:HOH906 2.5 36.7 1.0
O B:HOH921 2.6 34.8 1.0
C B:GLY43 3.5 13.4 1.0
S B:EPE406 3.7 30.1 0.7
CB B:ASP44 4.0 16.3 1.0
O3S B:EPE406 4.0 33.6 0.7
CA B:GLY43 4.3 12.9 1.0
O B:ASP44 4.3 15.1 1.0
C10 B:EPE406 4.4 29.2 0.7
N B:ASP44 4.4 13.1 1.0
O B:HOH810 4.4 43.0 1.0
N B:GLY43 4.4 13.5 1.0
OD2 B:ASP44 4.5 26.4 1.0
O B:HOH781 4.5 29.4 1.0
OD1 B:ASP68 4.5 20.9 1.0
C B:ASP44 4.5 13.6 1.0
CA B:ASP44 4.5 14.2 1.0
O2S B:EPE406 4.7 35.0 0.7
CG B:ASP44 4.8 23.4 1.0
O B:HOH557 4.9 16.5 1.0

Reference:

G.Minasov, Z.Wawrzak, P.J.Stogios, M.Kudritska, V.Yim, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.5 Angstrom Crystal Structure of Spermidine/Putrescine Abc Transporter Substrate-Binding Protein From Streptococcus Pneumoniae Strain Canada MDR_19A in Complex with Calcium and Hepes. To Be Published.
Page generated: Sun Jul 14 00:04:07 2024

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